[1] "ofn"        "-oTESCA-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/ESCA-TP/22506419/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/22588509/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=185, common to both=185
[1] "Reduce the number of clustering variables from 61 to 60."
[1]  60 185
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           153             32 
  TP53 MUTATED TP53 WILD-TYPE 
           153             32 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             172 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             172 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              19              166 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              19              166 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              16              169 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              16              169 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            32            153 
  MLL2 MUTATED MLL2 WILD-TYPE 
            32            153 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              175 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              175 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              15              170 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              15              170 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             172 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             172 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
             7            178 
  PKD2 MUTATED PKD2 WILD-TYPE 
             7            178 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              15              170 
  ARID1A MUTATED ARID1A WILD-TYPE 
              15              170 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             174 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             174 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             12             173 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             12             173 
[1] "KIAA2018 MUTATION ANALYSIS"
[1] 3
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                13                172 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                13                172 
[1] "FAM108A1 MUTATION ANALYSIS"
[1] 3
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 4                181 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 4                181 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              10              175 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              10              175 
[1] "MGC29506 MUTATION ANALYSIS"
[1] 3
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 4                181 
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 4                181 
[1] "C10ORF76 MUTATION ANALYSIS"
[1] 3
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 6                179 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 6                179 
[1] "IPP MUTATION ANALYSIS"
[1] 3
  IPP MUTATED IPP WILD-TYPE 
            6           179 
  IPP MUTATED IPP WILD-TYPE 
            6           179 
[1] "DNAH10 MUTATION ANALYSIS"
[1] 3
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              19              166 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              19              166 
[1] "RIC3 MUTATION ANALYSIS"
[1] 3
  RIC3 MUTATED RIC3 WILD-TYPE 
             4            181 
  RIC3 MUTATED RIC3 WILD-TYPE 
             4            181 
[1] "HMMR MUTATION ANALYSIS"
[1] 3
  HMMR MUTATED HMMR WILD-TYPE 
             4            181 
  HMMR MUTATED HMMR WILD-TYPE 
             4            181 
[1] "PIAS1 MUTATION ANALYSIS"
[1] 3
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              5             180 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              5             180 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              7             178 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              7             178 
[1] "ASTE1 MUTATION ANALYSIS"
[1] 3
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              5             180 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              5             180 
[1] "KPNA1 MUTATION ANALYSIS"
[1] 3
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             179 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             179 
[1] "LIMA1 MUTATION ANALYSIS"
[1] 3
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             177 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             177 
[1] "FAM65B MUTATION ANALYSIS"
[1] 3
  FAM65B MUTATED FAM65B WILD-TYPE 
               8              177 
  FAM65B MUTATED FAM65B WILD-TYPE 
               8              177 
[1] "CORO7 MUTATION ANALYSIS"
[1] 3
  CORO7 MUTATED CORO7 WILD-TYPE 
              7             178 
  CORO7 MUTATED CORO7 WILD-TYPE 
              7             178 
[1] "ANAPC1 MUTATION ANALYSIS"
[1] 3
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               5              180 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               5              180 
[1] "IVL MUTATION ANALYSIS"
[1] 3
  IVL MUTATED IVL WILD-TYPE 
           15           170 
  IVL MUTATED IVL WILD-TYPE 
           15           170 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              166 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              166 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
            7           178 
  RB1 MUTATED RB1 WILD-TYPE 
            7           178 
[1] "EIF4EBP2 MUTATION ANALYSIS"
[1] 3
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 3                182 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 3                182 
[1] "SCD MUTATION ANALYSIS"
[1] 3
  SCD MUTATED SCD WILD-TYPE 
            3           182 
  SCD MUTATED SCD WILD-TYPE 
            3           182 
[1] "MKL2 MUTATION ANALYSIS"
[1] 3
  MKL2 MUTATED MKL2 WILD-TYPE 
             6            179 
  MKL2 MUTATED MKL2 WILD-TYPE 
             6            179 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              18              167 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              18              167 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
             3            182 
  KLF3 MUTATED KLF3 WILD-TYPE 
             3            182 
[1] "IL10RA MUTATION ANALYSIS"
[1] 3
  IL10RA MUTATED IL10RA WILD-TYPE 
               3              182 
  IL10RA MUTATED IL10RA WILD-TYPE 
               3              182 
[1] "RAD17 MUTATION ANALYSIS"
[1] 3
  RAD17 MUTATED RAD17 WILD-TYPE 
              4             181 
  RAD17 MUTATED RAD17 WILD-TYPE 
              4             181 
[1] "KPNB1 MUTATION ANALYSIS"
[1] 3
  KPNB1 MUTATED KPNB1 WILD-TYPE 
              6             179 
  KPNB1 MUTATED KPNB1 WILD-TYPE 
              6             179 
[1] "ZBED4 MUTATION ANALYSIS"
[1] 3
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              5             180 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              5             180 
[1] "NAA16 MUTATION ANALYSIS"
[1] 3
  NAA16 MUTATED NAA16 WILD-TYPE 
              6             179 
  NAA16 MUTATED NAA16 WILD-TYPE 
              6             179 
[1] "CNNM2 MUTATION ANALYSIS"
[1] 3
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              7             178 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              7             178 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              7             178 
  HLA-B MUTATED HLA-B WILD-TYPE 
              7             178 
[1] "PLXNB2 MUTATION ANALYSIS"
[1] 3
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              12              173 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              12              173 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            178 
  PTEN MUTATED PTEN WILD-TYPE 
             7            178 
[1] "CPT1B MUTATION ANALYSIS"
[1] 3
  CPT1B MUTATED CPT1B WILD-TYPE 
              5             180 
  CPT1B MUTATED CPT1B WILD-TYPE 
              5             180 
[1] "CAMTA1 MUTATION ANALYSIS"
[1] 3
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
               9              176 
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
               9              176 
[1] "OTUD7B MUTATION ANALYSIS"
[1] 3
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               7              178 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               7              178 
[1] "ARRB1 MUTATION ANALYSIS"
[1] 3
  ARRB1 MUTATED ARRB1 WILD-TYPE 
              5             180 
  ARRB1 MUTATED ARRB1 WILD-TYPE 
              5             180 
[1] "KIAA1704 MUTATION ANALYSIS"
[1] 3
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 3                182 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 3                182 
[1] "RNF169 MUTATION ANALYSIS"
[1] 3
  RNF169 MUTATED RNF169 WILD-TYPE 
               6              179 
  RNF169 MUTATED RNF169 WILD-TYPE 
               6              179 
[1] "RBPJL MUTATION ANALYSIS"
[1] 3
  RBPJL MUTATED RBPJL WILD-TYPE 
              6             179 
  RBPJL MUTATED RBPJL WILD-TYPE 
              6             179 
[1] "MGAT5B MUTATION ANALYSIS"
[1] 3
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               8              177 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               8              177 
[1] "LRRC32 MUTATION ANALYSIS"
[1] 3
  LRRC32 MUTATED LRRC32 WILD-TYPE 
               9              176 
  LRRC32 MUTATED LRRC32 WILD-TYPE 
               9              176 
[1] "TCHH MUTATION ANALYSIS"
[1] 3
  TCHH MUTATED TCHH WILD-TYPE 
            14            171 
  TCHH MUTATED TCHH WILD-TYPE 
            14            171 
[1] "SLC22A2 MUTATION ANALYSIS"
[1] 3
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
                4               181 
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
                4               181 
[1] "PCDH15 MUTATION ANALYSIS"
[1] 3
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              21              164 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              21              164 
[1] "KIAA1549 MUTATION ANALYSIS"
[1] 3
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 8                177 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 8                177 
[1] "SETBP1 MUTATION ANALYSIS"
[1] 3
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              14              171 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              14              171 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 185 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=96,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 185 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "NUMBER_PACK_YEARS_SMOKED"   
[11] "RESIDUAL_TUMOR"              "NUMBER_OF_LYMPH_NODES"      
[13] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 31 43 88  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   32    43    88     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 31 43 88  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   32    43    88     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
77 69 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
77 69 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
77 69 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
77 69 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=46, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=14, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   90 63
  TP53 WILD-TYPE 18 14
  TP53 MUTATED TP53 WILD-TYPE 
           153             32 
  TP53 MUTATED TP53 WILD-TYPE 
            63             14 
$`TP53 MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GG TCGA-2H-A9GH 
       35.97        27.12         5.16        20.02        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
       17.03         0.79        23.41        12.82         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C 
       47.38        21.70        23.18        31.56        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH 
       15.48         2.60         7.40         3.75         3.02        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.48        16.47        13.55        13.22        21.37        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       33.11         8.02         7.59         5.06        16.31         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW 
       53.95         9.30        15.78         2.89        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        2.10         1.32         2.66 

$`TP53 WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-2H-A9GF 
       15.68         8.94        19.99        22.82         0.36        25.78 
TCGA-2H-A9GI TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FE TCGA-JY-A93F TCGA-KH-A6WC 
       14.30         9.30        14.86         3.68        24.03         6.28 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A8NE 
       32.61         3.32        58.59         7.43        25.12        55.50 
TCGA-L5-A8NF TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-Q9-A6FW 
        2.66         7.76         5.49         8.71        83.24         7.82 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8ET 
        7.04        38.40         2.30         7.00        15.35         1.55 
TCGA-VR-AA7I TCGA-ZR-A9CJ 
       15.91        19.73 

  TP53 MUTATED TP53 WILD-TYPE 
          0.13           0.36 
  TP53 MUTATED TP53 WILD-TYPE 
        122.10          83.24 
  TP53 MUTATED TP53 WILD-TYPE 
         13.15          11.80 
[1] "0.1 - 122.1 (13.2)" "0.4 - 83.2 (11.8)" 
[1] "hr=" "1"  
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53 MUTATED         7        3        5        1        43        24
  TP53 WILD-TYPE       1        2        1        0         4         7
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED          20         13          8          4        5         3
  TP53 WILD-TYPE         6          1          1          3        0         1
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               7              1
  STAGE IA              3              2
  STAGE IB              5              1
  STAGE II              1              0
  STAGE IIA            43              4
  STAGE IIB            24              7
  STAGE III            20              6
  STAGE IIIA           13              1
  STAGE IIIB            8              1
  STAGE IIIC            4              3
  STAGE IV              5              0
  STAGE IVA             3              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  TP53 MUTATED      26 35 75  3
  TP53 WILD-TYPE     6  8 13  2
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           26              6
  T2              35              8
  T3              75             13
  T4               3              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   65 58 10  5
  TP53 WILD-TYPE 12 11  2  3
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           65             12
  N1           58             11
  N2           10              2
  N3            5              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED   115   8
  TP53 WILD-TYPE  21   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    115    8
  TP53 WILD-TYPE   21    1
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          115             21
  1            8              1
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    19 134
  TP53 WILD-TYPE   8  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19  134
  TP53 WILD-TYPE    8   24
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           19              8
  MALE            134             24
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   100  39
  TP53 WILD-TYPE  24   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    100   39
  TP53 WILD-TYPE   24    4
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           100             24
  YES           39              4
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, binary
                cls
clus              0  1
  TP53 MUTATED   66 87
  TP53 WILD-TYPE 23  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     66   87
  TP53 WILD-TYPE   23    9
                                   clus
vv                                  TP53 MUTATED TP53 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS               66             23
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           87              9
[1] 2 2
[1] FALSE
D1V11, continuous
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   115  11   1   5
  TP53 WILD-TYPE  22   2   1   2
D1V12, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          115             22
  R1           11              2
  R2            1              1
  RX            5              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED      46                         4    87
  TP53 WILD-TYPE     0                         1    27
D1V14, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                               46              0
  BLACK OR AFRICAN AMERICAN            4              1
  WHITE                               87             27
[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"
D1V15, binary
                cls
clus              0  1
  TP53 MUTATED    6 77
  TP53 WILD-TYPE  0 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6   77
  TP53 WILD-TYPE    0   11
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                6              0
  NOT HISPANIC OR LATINO           77             11
[1] 2 2
[1] FALSE

Clustering(2) Variable = SMAD4 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED     5   8
  SMAD4 WILD-TYPE 103  69
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             13             172 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              69 
$`SMAD4 MUTATED`
TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-2H-A9GN TCGA-IC-A6RE TCGA-JY-A93C TCGA-L5-A4OR 
       24.00         5.16         8.94         7.69        23.18         3.16 
TCGA-L5-A8NU TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-VR-A8EQ TCGA-VR-AA7D 
       83.24         5.06        53.95         2.30        22.82         9.17 
TCGA-Z6-AAPN 
        2.66 

$`SMAD4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94        16.24         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        3.42         2.10         1.32        19.73 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           2.30            0.13 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          83.24          122.10 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
           8.94           13.18 
[1] "2.3 - 83.2 (8.9)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "1.4"
D2V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD4 MUTATED         0        1        0        0         2         1
  SMAD4 WILD-TYPE       8        4        6        1        45        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED           2          0          3          1        0         0
  SMAD4 WILD-TYPE        24         14          6          6        5         4
D2V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0               8
  STAGE IA               1               4
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              2              45
  STAGE IIB              1              30
  STAGE III              2              24
  STAGE IIIA             0              14
  STAGE IIIB             3               6
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  SMAD4 MUTATED       2  1  7  0
  SMAD4 WILD-TYPE    30 42 81  5
D2V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T0+T1             2              30
  T2                1              42
  T3                7              81
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  SMAD4 MUTATED    3  3  3  1
  SMAD4 WILD-TYPE 74 66  9  7
D2V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             3              74
  N1             3              66
  N2             3               9
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED     8   0
  SMAD4 WILD-TYPE 128   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      8    0
  SMAD4 WILD-TYPE  128    9
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             8             128
  1             0               9
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED     1  12
  SMAD4 WILD-TYPE  26 146
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1   12
  SMAD4 WILD-TYPE   26  146
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             1              26
  MALE              12             146
[1] 2 2
[1] FALSE
D2V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED     9   2
  SMAD4 WILD-TYPE 115  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      9    2
  SMAD4 WILD-TYPE  115   41
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO              9             115
  YES             2              41
[1] 2 2
[1] FALSE
D2V9, continuous
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D2V10, binary
                 cls
clus               0  1
  SMAD4 MUTATED   10  3
  SMAD4 WILD-TYPE 79 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     10    3
  SMAD4 WILD-TYPE   79   93
                                   clus
vv                                  SMAD4 MUTATED SMAD4 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                10              79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             3              93
[1] 2 2
[1] FALSE
D2V11, continuous
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED     8   0   0   2
  SMAD4 WILD-TYPE 129  13   2   5
D2V12, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0             8             129
  R1             0              13
  R2             0               2
  RX             2               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       1                         0    10
  SMAD4 WILD-TYPE    45                         5   104
D2V14, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                 cls
clus               0  1
  SMAD4 MUTATED    0  6
  SMAD4 WILD-TYPE  6 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0    6
  SMAD4 WILD-TYPE    6   82
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6              82
[1] 2 2
[1] FALSE

Clustering(3) Variable = CDKN2A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED   13  6
  CDKN2A WILD-TYPE 95 71
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              19              166 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               6               71 
$`CDKN2A MUTATED`
TCGA-L5-A8NG TCGA-2H-A9GN TCGA-JY-A93D TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OP 
       35.97         8.94        31.56        26.33         3.32         7.17 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49O 
       13.22         7.76         5.49        13.41        10.36        13.41 
TCGA-LN-A49R TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-V5-A7RC TCGA-VR-AA4D 
       13.38        13.18        33.11        38.40         3.42        46.19 
TCGA-XP-A8T7 
       41.23 

$`CDKN2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93        18.35         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48        16.47        13.55        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            3.32             0.13 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           46.19           122.10 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           13.38            12.85 
[1] "3.3 - 46.2 (13.4)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.5"
D3V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKN2A MUTATED         0        1        0        0         4         4
  CDKN2A WILD-TYPE       8        4        6        1        43        27
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED           5          0          0          3        0
  CDKN2A WILD-TYPE        21         14          9          4        5
                  vv
clus               STAGE IVA
  CDKN2A MUTATED           0
  CDKN2A WILD-TYPE         4
D3V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                8
  STAGE IA                1                4
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               4               43
  STAGE IIB               4               27
  STAGE III               5               21
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              3                4
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  CDKN2A MUTATED       3  4 10  0
  CDKN2A WILD-TYPE    29 39 78  5
D3V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1              3               29
  T2                 4               39
  T3                10               78
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDKN2A MUTATED    6  8  0  3
  CDKN2A WILD-TYPE 71 61 12  5
D3V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0              6               71
  N1              8               61
  N2              0               12
  N3              3                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    14   0
  CDKN2A WILD-TYPE 122   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     14    0
  CDKN2A WILD-TYPE  122    9
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             14              122
  1              0                9
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     4  15
  CDKN2A WILD-TYPE  23 143
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      4   15
  CDKN2A WILD-TYPE   23  143
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              4               23
  MALE               15              143
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     8   8
  CDKN2A WILD-TYPE 116  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8    8
  CDKN2A WILD-TYPE  116   35
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO               8              116
  YES              8               35
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, binary
                  cls
clus                0  1
  CDKN2A MUTATED   14  5
  CDKN2A WILD-TYPE 75 91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     14    5
  CDKN2A WILD-TYPE   75   91
                                   clus
vv                                  CDKN2A MUTATED CDKN2A WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 14               75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              5               91
[1] 2 2
[1] FALSE
D3V11, continuous
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED    15   0   0   0
  CDKN2A WILD-TYPE 122  13   2   7
D3V12, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             15              122
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       3                         1    13
  CDKN2A WILD-TYPE    43                         4   101
D3V14, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  3               43
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                 13              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                  cls
clus                0  1
  CDKN2A MUTATED    1  6
  CDKN2A WILD-TYPE  5 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1    6
  CDKN2A WILD-TYPE    5   82
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              6               82
[1] 2 2
[1] FALSE

Clustering(4) Variable = NFE2L2 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED   11  5
  NFE2L2 WILD-TYPE 97 72
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              16              169 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               5               72 
$`NFE2L2 MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A8O2 TCGA-L5-A88Z TCGA-LN-A49R 
       35.21         0.53        12.82         4.67         7.40        13.38 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.22         4.47        25.25        12.00        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-VR-A8ER TCGA-ZR-A9CJ 
       13.38        13.18        12.43        19.73 

$`NFE2L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
       17.03         0.79        23.41         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
       12.33        12.33        10.52        12.23        12.03         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN 
        2.66 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.53             0.13 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           35.21           122.10 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           13.00            13.15 
[1] "0.5 - 35.2 (13.0)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D4V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFE2L2 MUTATED         0        0        0        0         9         0
  NFE2L2 WILD-TYPE       8        5        6        1        38        31
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFE2L2 MUTATED           2          1          2          1        1
  NFE2L2 WILD-TYPE        24         13          7          6        4
                  vv
clus               STAGE IVA
  NFE2L2 MUTATED           0
  NFE2L2 WILD-TYPE         4
D4V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               9               38
  STAGE IIB               0               31
  STAGE III               2               24
  STAGE IIIA              1               13
  STAGE IIIB              2                7
  STAGE IIIC              1                6
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  NFE2L2 MUTATED       1  8  6  1
  NFE2L2 WILD-TYPE    31 35 82  4
D4V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1              1               31
  T2                 8               35
  T3                 6               82
  T4                 1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NFE2L2 MUTATED    8  5  2  1
  NFE2L2 WILD-TYPE 69 64 10  7
D4V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              8               69
  N1              5               64
  N2              2               10
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    14   1
  NFE2L2 WILD-TYPE 122   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     14    1
  NFE2L2 WILD-TYPE  122    8
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             14              122
  1              1                8
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     2  14
  NFE2L2 WILD-TYPE  25 144
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      2   14
  NFE2L2 WILD-TYPE   25  144
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              2               25
  MALE               14              144
[1] 2 2
[1] FALSE
D4V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     9   4
  NFE2L2 WILD-TYPE 115  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      9    4
  NFE2L2 WILD-TYPE  115   39
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               9              115
  YES              4               39
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    1 15
  NFE2L2 WILD-TYPE 88 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      1   15
  NFE2L2 WILD-TYPE   88   81
                                   clus
vv                                  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  1               88
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             15               81
[1] 2 2
[1] FALSE
D4V11, continuous
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    14   1   1   0
  NFE2L2 WILD-TYPE 123  12   1   7
D4V12, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             14              123
  R1              1               12
  R2              1                1
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED      12                         0     3
  NFE2L2 WILD-TYPE    34                         5   111
D4V14, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                 12               34
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[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"
D4V15, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    0 14
  NFE2L2 WILD-TYPE  6 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   14
  NFE2L2 WILD-TYPE    6   74
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             14               74
[1] 2 2
[1] FALSE

Clustering(5) Variable = MLL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   21 11
  MLL2 WILD-TYPE 87 66
  MLL2 MUTATED MLL2 WILD-TYPE 
            32            153 
  MLL2 MUTATED MLL2 WILD-TYPE 
            11             66 
$`MLL2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OG TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A625 
        4.31         4.70         7.63        13.94         8.94        12.82 
TCGA-JY-A6FD TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A88V 
       68.02        31.56        24.03         6.28        30.25         2.60 
TCGA-L5-A88W TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49R TCGA-LN-A49S 
       25.12         7.76         8.71        46.09        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ 
       15.35        12.59        12.76         4.47        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6XG TCGA-VR-A8EU 
       12.33        13.18         0.13        12.03        38.40        18.31 
TCGA-XP-A8T7 TCGA-Z6-AAPN 
       41.23         2.66 

$`MLL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        5.92        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       25.22         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49V 
       10.45        12.66        12.43        13.41        12.33        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.62        12.46        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.85        15.52        11.54        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FQ 
       25.25        10.52        12.00        12.03        13.38        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        2.10         1.32        19.73 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.13           0.30 
  MLL2 MUTATED MLL2 WILD-TYPE 
         68.02         122.10 
  MLL2 MUTATED MLL2 WILD-TYPE 
         12.79          13.22 
[1] "0.1 - 68.0 (12.8)"  "0.3 - 122.1 (13.2)"
[1] "hr=" "1.1"
D5V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL2 MUTATED         2        1        2        0        13         3
  MLL2 WILD-TYPE       6        4        4        1        34        28
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL2 MUTATED           6          0          1          1        2         0
  MLL2 WILD-TYPE        20         14          8          6        3         4
D5V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               2              6
  STAGE IA              1              4
  STAGE IB              2              4
  STAGE II              0              1
  STAGE IIA            13             34
  STAGE IIB             3             28
  STAGE III             6             20
  STAGE IIIA            0             14
  STAGE IIIB            1              8
  STAGE IIIC            1              6
  STAGE IV              2              3
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  MLL2 MUTATED       5 11 15  0
  MLL2 WILD-TYPE    27 32 73  5
D5V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T0+T1            5             27
  T2              11             32
  T3              15             73
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   18 11  1  1
  MLL2 WILD-TYPE 59 58 11  7
D5V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           18             59
  N1           11             58
  N2            1             11
  N3            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                cls
clus               0   1
  MLL2 MUTATED    26   2
  MLL2 WILD-TYPE 110   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     26    2
  MLL2 WILD-TYPE  110    7
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           26            110
  1            2              7
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  MLL2 MUTATED     8  24
  MLL2 WILD-TYPE  19 134
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      8   24
  MLL2 WILD-TYPE   19  134
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE            8             19
  MALE             24            134
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus               0   1
  MLL2 MUTATED    18  12
  MLL2 WILD-TYPE 106  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     18   12
  MLL2 WILD-TYPE  106   31
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            18            106
  YES           12             31
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, binary
                cls
clus              0  1
  MLL2 MUTATED   11 21
  MLL2 WILD-TYPE 78 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     11   21
  MLL2 WILD-TYPE   78   75
                                   clus
vv                                  MLL2 MUTATED MLL2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS               11             78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           21             75
[1] 2 2
[1] FALSE
D5V11, continuous
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    26   1   1   1
  MLL2 WILD-TYPE 111  12   1   6
D5V12, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           26            111
  R1            1             12
  R2            1              1
  RX            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED      14                         0    14
  MLL2 WILD-TYPE    32                         5   100
D5V14, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                               14             32
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               14            100
[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"
D5V15, binary
                cls
clus              0  1
  MLL2 MUTATED    1 16
  MLL2 WILD-TYPE  5 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   16
  MLL2 WILD-TYPE    5   72
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           16             72
[1] 2 2
[1] FALSE

Clustering(6) Variable = ZNF750 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED     8   2
  ZNF750 WILD-TYPE 100  75
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              10              175 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2               75 
$`ZNF750 MUTATED`
TCGA-S8-A6BV TCGA-IG-A8O2 TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A9 TCGA-LN-A7HV 
       20.02         4.67        13.15        12.46        11.54        10.52 
TCGA-LN-A7HX TCGA-LN-A9FP TCGA-Z6-A8JD TCGA-Z6-A8JE 
       12.23        12.03         3.42         2.10 

$`ZNF750 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        25.08        41.23        14.37         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
            2.10             0.13 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           20.02           122.10 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
          11.785           13.220 
[1] "2.1 - 20.0 (11.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D6V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF750 MUTATED         0        0        0        0         6         1
  ZNF750 WILD-TYPE       8        5        6        1        41        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF750 MUTATED           0          2          1          0        0
  ZNF750 WILD-TYPE        26         12          8          7        5
                  vv
clus               STAGE IVA
  ZNF750 MUTATED           0
  ZNF750 WILD-TYPE         4
D6V3, multiclass
            clus
vv           ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               6               41
  STAGE IIB               1               30
  STAGE III               0               26
  STAGE IIIA              2               12
  STAGE IIIB              1                8
  STAGE IIIC              0                7
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  ZNF750 MUTATED       0  4  6  0
  ZNF750 WILD-TYPE    32 39 82  5
D6V4, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T0+T1              0               32
  T2                 4               39
  T3                 6               82
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF750 MUTATED    7  2  1  0
  ZNF750 WILD-TYPE 70 67 11  8
D6V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              7               70
  N1              2               67
  N2              1               11
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     9   0
  ZNF750 WILD-TYPE 127   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      9    0
  ZNF750 WILD-TYPE  127    9
   clus
vv  ZNF750 MUTATED ZNF750 WILD-TYPE
  0              9              127
  1              0                9
[1] 2 2
[1] FALSE
D6V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     1   9
  ZNF750 WILD-TYPE  26 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      1    9
  ZNF750 WILD-TYPE   26  149
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              1               26
  MALE                9              149
[1] 2 2
[1] FALSE
D6V8, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     5   4
  ZNF750 WILD-TYPE 119  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      5    4
  ZNF750 WILD-TYPE  119   39
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO               5              119
  YES              4               39
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, binary
                  cls
clus                0  1
  ZNF750 MUTATED    1  9
  ZNF750 WILD-TYPE 88 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      1    9
  ZNF750 WILD-TYPE   88   87
                                   clus
vv                                  ZNF750 MUTATED ZNF750 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  1               88
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              9               87
[1] 2 2
[1] FALSE
D6V11, continuous
                  vv
clus                R0  R1  R2  RX
  ZNF750 MUTATED     9   0   0   1
  ZNF750 WILD-TYPE 128  13   2   6
D6V12, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  R0              9              128
  R1              0               13
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF750 MUTATED       7                         0     3
  ZNF750 WILD-TYPE    39                         5   111
D6V14, multiclass
                           clus
vv                          ZNF750 MUTATED ZNF750 WILD-TYPE
  ASIAN                                  7               39
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[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"
D6V15, binary
                  cls
clus                0  1
  ZNF750 MUTATED    0 10
  ZNF750 WILD-TYPE  6 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   10
  ZNF750 WILD-TYPE    6   78
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10               78
[1] 2 2
[1] FALSE

Clustering(7) Variable = TGFBR2 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  TGFBR2 MUTATED   11  4
  TGFBR2 WILD-TYPE 97 73
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              15              170 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               4               73 
$`TGFBR2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A4OO TCGA-L5-A88W 
        4.31        19.99        24.03        30.25         3.32        25.12 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A7HZ 
        7.76         8.71        10.36        12.43        12.33        13.18 
TCGA-VR-A8EX TCGA-VR-AA4G TCGA-Z6-A9VB 
       28.11        18.05         1.32 

$`TGFBR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       25.22         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.66        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1.32             0.13 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           30.25           122.10 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          12.430           13.165 
[1] "1.3 - 30.2 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D7V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TGFBR2 MUTATED         1        0        1        0         3         3
  TGFBR2 WILD-TYPE       7        5        5        1        44        28
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           1          2          0          3        0
  TGFBR2 WILD-TYPE        25         12          9          4        5
                  vv
clus               STAGE IVA
  TGFBR2 MUTATED           1
  TGFBR2 WILD-TYPE         3
D7V3, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               3               44
  STAGE IIB               3               28
  STAGE III               1               25
  STAGE IIIA              2               12
  STAGE IIIB              0                9
  STAGE IIIC              3                4
  STAGE IV                0                5
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  TGFBR2 MUTATED       2  5  8  0
  TGFBR2 WILD-TYPE    30 38 80  5
D7V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T0+T1              2               30
  T2                 5               38
  T3                 8               80
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TGFBR2 MUTATED    6  5  1  3
  TGFBR2 WILD-TYPE 71 64 11  5
D7V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              6               71
  N1              5               64
  N2              1               11
  N3              3                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    10   1
  TGFBR2 WILD-TYPE 126   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     10    1
  TGFBR2 WILD-TYPE  126    8
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             10              126
  1              1                8
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     4  11
  TGFBR2 WILD-TYPE  23 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      4   11
  TGFBR2 WILD-TYPE   23  147
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              4               23
  MALE               11              147
[1] 2 2
[1] FALSE
D7V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    10   3
  TGFBR2 WILD-TYPE 114  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     10    3
  TGFBR2 WILD-TYPE  114   40
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO              10              114
  YES              3               40
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    6  9
  TGFBR2 WILD-TYPE 83 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      6    9
  TGFBR2 WILD-TYPE   83   87
                                   clus
vv                                  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  6               83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              9               87
[1] 2 2
[1] FALSE
D7V11, continuous
                  vv
clus                R0  R1  R2  RX
  TGFBR2 MUTATED    13   1   0   1
  TGFBR2 WILD-TYPE 124  12   2   6
D7V12, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0             13              124
  R1              1               12
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED       3                         0    10
  TGFBR2 WILD-TYPE    43                         5   104
D7V14, multiclass
                           clus
vv                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                  3               43
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    0  5
  TGFBR2 WILD-TYPE  6 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    5
  TGFBR2 WILD-TYPE    6   83
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5               83
[1] 2 2
[1] FALSE

Clustering(8) Variable = FBXW7 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED     7   6
  FBXW7 WILD-TYPE 101  71
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             172 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              6              71 
$`FBXW7 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GN TCGA-IG-A3YB TCGA-IG-A7DP TCGA-L5-A88Z TCGA-L5-A8NI 
       19.99         8.94         2.63        14.86         7.40        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-LN-A8HZ TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-V5-A7RB 
        7.76         5.49        12.33        16.31        15.78         5.29 
TCGA-XP-A8T7 
       41.23 

$`FBXW7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ 
        2.66        12.92        16.47        13.55        13.22        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           2.63            0.13 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          41.23          122.10 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         12.330          13.165 
[1] "2.6 - 41.2 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.6"
D8V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXW7 MUTATED         0        0        0        0         3         1
  FBXW7 WILD-TYPE       8        5        6        1        44        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED           3          2          0          1        0         1
  FBXW7 WILD-TYPE        23         12          9          6        5         3
D8V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              3              44
  STAGE IIB              1              30
  STAGE III              3              23
  STAGE IIIA             2              12
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  FBXW7 MUTATED       2  3  6  1
  FBXW7 WILD-TYPE    30 40 82  4
D8V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1             2              30
  T2                3              40
  T3                6              82
  T4                1               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FBXW7 MUTATED    2  8  0  1
  FBXW7 WILD-TYPE 75 61 12  7
D8V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             2              75
  N1             8              61
  N2             0              12
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED     8   1
  FBXW7 WILD-TYPE 128   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      8    1
  FBXW7 WILD-TYPE  128    8
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             8             128
  1             1               8
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED     4   9
  FBXW7 WILD-TYPE  23 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      4    9
  FBXW7 WILD-TYPE   23  149
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             4              23
  MALE               9             149
[1] 2 2
[1] FALSE
D8V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    11   2
  FBXW7 WILD-TYPE 113  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     11    2
  FBXW7 WILD-TYPE  113   41
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             11             113
  YES             2              41
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, binary
                 cls
clus               0  1
  FBXW7 MUTATED    9  4
  FBXW7 WILD-TYPE 80 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      9    4
  FBXW7 WILD-TYPE   80   92
                                   clus
vv                                  FBXW7 MUTATED FBXW7 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 9              80
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             4              92
[1] 2 2
[1] FALSE
D8V11, continuous
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    10   0   0   0
  FBXW7 WILD-TYPE 127  13   2   7
D8V12, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            10             127
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       1                         0    10
  FBXW7 WILD-TYPE    45                         5   104
D8V14, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                 cls
clus               0  1
  FBXW7 MUTATED    2  5
  FBXW7 WILD-TYPE  4 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2    5
  FBXW7 WILD-TYPE    4   83
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO             5              83
[1] 2 2
[1] FALSE

Clustering(9) Variable = PKD2 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  PKD2 MUTATED     6   1
  PKD2 WILD-TYPE 102  76
  PKD2 MUTATED PKD2 WILD-TYPE 
             7            178 
  PKD2 MUTATED PKD2 WILD-TYPE 
             1             76 
$`PKD2 MUTATED`
TCGA-IG-A4P3 TCGA-L5-A8NL TCGA-L5-A8NS TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A8 
       18.64        13.22        13.41        12.59        12.49        15.52 
TCGA-LN-A9FQ 
       12.85 

$`PKD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.59        12.76        12.59        22.39        12.85        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  PKD2 MUTATED PKD2 WILD-TYPE 
         12.49           0.13 
  PKD2 MUTATED PKD2 WILD-TYPE 
         18.64         122.10 
  PKD2 MUTATED PKD2 WILD-TYPE 
        13.220         13.035 
[1] "12.5 - 18.6 (13.2)" "0.1 - 122.1 (13.0)"
[1] "hr=" "2.3"
D9V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKD2 MUTATED         0        0        0        0         4         2
  PKD2 WILD-TYPE       8        5        6        1        43        29
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKD2 MUTATED           1          0          0          0        0         0
  PKD2 WILD-TYPE        25         14          9          7        5         4
D9V3, multiclass
            clus
vv           PKD2 MUTATED PKD2 WILD-TYPE
  STAGE I               0              8
  STAGE IA              0              5
  STAGE IB              0              6
  STAGE II              0              1
  STAGE IIA             4             43
  STAGE IIB             2             29
  STAGE III             1             25
  STAGE IIIA            0             14
  STAGE IIIB            0              9
  STAGE IIIC            0              7
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  PKD2 MUTATED       0  2  5  0
  PKD2 WILD-TYPE    32 41 83  5
D9V4, multiclass
       clus
vv      PKD2 MUTATED PKD2 WILD-TYPE
  T0+T1            0             32
  T2               2             41
  T3               5             83
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PKD2 MUTATED    5  2  0  0
  PKD2 WILD-TYPE 72 67 12  8
D9V5, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  N0            5             72
  N1            2             67
  N2            0             12
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                cls
clus               0   1
  PKD2 MUTATED     7   0
  PKD2 WILD-TYPE 129   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      7    0
  PKD2 WILD-TYPE  129    9
   clus
vv  PKD2 MUTATED PKD2 WILD-TYPE
  0            7            129
  1            0              9
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  PKD2 MUTATED     0   7
  PKD2 WILD-TYPE  27 151
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      0    7
  PKD2 WILD-TYPE   27  151
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  FEMALE            0             27
  MALE              7            151
[1] 2 2
[1] FALSE
D9V8, binary
                cls
clus               0   1
  PKD2 MUTATED     2   4
  PKD2 WILD-TYPE 122  39
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      2    4
  PKD2 WILD-TYPE  122   39
     clus
vv    PKD2 MUTATED PKD2 WILD-TYPE
  NO             2            122
  YES            4             39
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, binary
                cls
clus              0  1
  PKD2 MUTATED    2  5
  PKD2 WILD-TYPE 87 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      2    5
  PKD2 WILD-TYPE   87   91
                                   clus
vv                                  PKD2 MUTATED PKD2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                2             87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            5             91
[1] 2 2
[1] FALSE
D9V11, continuous
                vv
clus              R0  R1  R2  RX
  PKD2 MUTATED     7   0   0   0
  PKD2 WILD-TYPE 130  13   2   7
D9V12, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  R0            7            130
  R1            0             13
  R2            0              2
  RX            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PKD2 MUTATED       4                         0     3
  PKD2 WILD-TYPE    42                         5   111
D9V14, multiclass
                           clus
vv                          PKD2 MUTATED PKD2 WILD-TYPE
  ASIAN                                4             42
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[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"
D9V15, binary
                cls
clus              0  1
  PKD2 MUTATED    0  5
  PKD2 WILD-TYPE  6 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      0    5
  PKD2 WILD-TYPE    6   83
                        clus
vv                       PKD2 MUTATED PKD2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5             83
[1] 2 2
[1] FALSE

Clustering(10) Variable = ARID1A MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     7   8
  ARID1A WILD-TYPE 101  69
  ARID1A MUTATED ARID1A WILD-TYPE 
              15              170 
  ARID1A MUTATED ARID1A WILD-TYPE 
               8               69 
$`ARID1A MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-2H-A9GF TCGA-2H-A9GR TCGA-JY-A6FA TCGA-JY-A6FH 
       24.00        19.99        25.78        32.45        44.75        47.38 
TCGA-JY-A939 TCGA-JY-A93F TCGA-L5-A4OJ TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A8NL 
       21.70        24.03        21.01         7.43         7.40        13.22 
TCGA-R6-A6DQ TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59         9.30         7.00 

$`ARID1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93C 
       12.16       122.10        68.02         3.68        41.52        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  ARID1A MUTATED ARID1A WILD-TYPE 
            7.00             0.13 
  ARID1A MUTATED ARID1A WILD-TYPE 
           47.38           122.10 
  ARID1A MUTATED ARID1A WILD-TYPE 
           21.01            12.85 
[1] "7.0 - 47.4 (21.0)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D10V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1A MUTATED         1        0        1        0         2         5
  ARID1A WILD-TYPE       7        5        5        1        45        26
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           2          0          1          1        0
  ARID1A WILD-TYPE        24         14          8          6        5
                  vv
clus               STAGE IVA
  ARID1A MUTATED           0
  ARID1A WILD-TYPE         4
D10V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               2               45
  STAGE IIB               5               26
  STAGE III               2               24
  STAGE IIIA              0               14
  STAGE IIIB              1                8
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  ARID1A MUTATED       4  4  5  0
  ARID1A WILD-TYPE    28 39 83  5
D10V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T0+T1              4               28
  T2                 4               39
  T3                 5               83
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ARID1A MUTATED    3  8  1  1
  ARID1A WILD-TYPE 74 61 11  7
D10V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              3               74
  N1              8               61
  N2              1               11
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    11   0
  ARID1A WILD-TYPE 125   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     11    0
  ARID1A WILD-TYPE  125    9
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             11              125
  1              0                9
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     5  10
  ARID1A WILD-TYPE  22 148
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5   10
  ARID1A WILD-TYPE   22  148
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              5               22
  MALE               10              148
[1] 2 2
[1] FALSE
D10V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    13   0
  ARID1A WILD-TYPE 111  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     13    0
  ARID1A WILD-TYPE  111   43
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              13              111
  YES              0               43
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, binary
                  cls
clus                0  1
  ARID1A MUTATED   12  3
  ARID1A WILD-TYPE 77 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     12    3
  ARID1A WILD-TYPE   77   93
                                   clus
vv                                  ARID1A MUTATED ARID1A WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 12               77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              3               93
[1] 2 2
[1] FALSE
D10V11, continuous
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    10   2   0   1
  ARID1A WILD-TYPE 127  11   2   6
D10V12, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             10              127
  R1              2               11
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       1                         0    12
  ARID1A WILD-TYPE    45                         5   102
D10V14, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  1               45
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 12              102
[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"
D10V15, binary
                  cls
clus                0  1
  ARID1A MUTATED    1  2
  ARID1A WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1    2
  ARID1A WILD-TYPE    5   86
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              2               86
[1] 2 2
[1] FALSE

Clustering(11) Variable = ERBB2 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     5   6
  ERBB2 WILD-TYPE 103  71
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             174 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              6              71 
$`ERBB2 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-2H-A9GH TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A8NM 
       34.85        19.99        31.27        29.00         2.60         7.76 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.59         5.06         2.89         2.30        12.69 

$`ERBB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        20.05        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30        15.78         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           2.30            0.13 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          34.85          122.10 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
           7.76           13.18 
[1] "2.3 - 34.9 (7.8)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "1.7"
D11V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB2 MUTATED         0        0        0        0         1         3
  ERBB2 WILD-TYPE       8        5        6        1        46        28
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED           1          0          0          1        0         0
  ERBB2 WILD-TYPE        25         14          9          6        5         4
D11V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              3              28
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  ERBB2 MUTATED       1  1  4  0
  ERBB2 WILD-TYPE    31 42 84  5
D11V4, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  T0+T1             1              31
  T2                1              42
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERBB2 MUTATED    2  3  0  1
  ERBB2 WILD-TYPE 75 66 12  7
D11V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             2              75
  N1             3              66
  N2             0              12
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED     4   0
  ERBB2 WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      4    0
  ERBB2 WILD-TYPE  132    9
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     2   9
  ERBB2 WILD-TYPE  25 149
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      2    9
  ERBB2 WILD-TYPE   25  149
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             2              25
  MALE               9             149
[1] 2 2
[1] FALSE
D11V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED     9   0
  ERBB2 WILD-TYPE 115  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      9    0
  ERBB2 WILD-TYPE  115   43
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              9             115
  YES             0              43
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, binary
                 cls
clus               0  1
  ERBB2 MUTATED   11  0
  ERBB2 WILD-TYPE 78 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     11    0
  ERBB2 WILD-TYPE   78   96
                                   clus
vv                                  ERBB2 MUTATED ERBB2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                11              78
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             0              96
[1] 2 2
[1] FALSE
D11V11, continuous
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED     6   0   0   0
  ERBB2 WILD-TYPE 131  13   2   7
D11V12, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             6             131
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED       0                         0    10
  ERBB2 WILD-TYPE    46                         5   104
D11V14, multiclass
                           clus
vv                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                 0              46
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                 cls
clus               0  1
  ERBB2 MUTATED    1  4
  ERBB2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1    4
  ERBB2 WILD-TYPE    5   84
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             4              84
[1] 2 2
[1] FALSE

Clustering(12) Variable = PTCH1 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED     5   7
  PTCH1 WILD-TYPE 103  70
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             12             173 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7              70 
$`PTCH1 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-IG-A3QL TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A8NM 
        4.31        19.99        35.21        44.75        25.22         7.76 
TCGA-L5-A8NQ TCGA-LN-A49R TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8EW TCGA-XP-A8T8 
       21.37        13.38         3.42        18.31         8.12        14.37 

$`PTCH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           3.42            0.13 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          44.75          122.10 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          16.34           12.85 
[1] "3.4 - 44.8 (16.3)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D12V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTCH1 MUTATED         0        0        0        0         2         4
  PTCH1 WILD-TYPE       8        5        6        1        45        27
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH1 MUTATED           1          1          1          1        1         0
  PTCH1 WILD-TYPE        25         13          8          6        4         4
D12V3, multiclass
            clus
vv           PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              2              45
  STAGE IIB              4              27
  STAGE III              1              25
  STAGE IIIA             1              13
  STAGE IIIB             1               8
  STAGE IIIC             1               6
  STAGE IV               1               4
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  PTCH1 MUTATED       2  4  5  0
  PTCH1 WILD-TYPE    30 39 83  5
D12V4, multiclass
       clus
vv      PTCH1 MUTATED PTCH1 WILD-TYPE
  T0+T1             2              30
  T2                4              39
  T3                5              83
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PTCH1 MUTATED    3  6  1  1
  PTCH1 WILD-TYPE 74 63 11  7
D12V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0             3              74
  N1             6              63
  N2             1              11
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED     8   1
  PTCH1 WILD-TYPE 128   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      8    1
  PTCH1 WILD-TYPE  128    8
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0             8             128
  1             1               8
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED     1  11
  PTCH1 WILD-TYPE  26 147
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      1   11
  PTCH1 WILD-TYPE   26  147
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE             1              26
  MALE              11             147
[1] 2 2
[1] FALSE
D12V8, binary
                 cls
clus                0   1
  PTCH1 MUTATED     7   4
  PTCH1 WILD-TYPE 117  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      7    4
  PTCH1 WILD-TYPE  117   39
     clus
vv    PTCH1 MUTATED PTCH1 WILD-TYPE
  NO              7             117
  YES             4              39
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, binary
                 cls
clus               0  1
  PTCH1 MUTATED    3  9
  PTCH1 WILD-TYPE 86 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    9
  PTCH1 WILD-TYPE   86   87
                                   clus
vv                                  PTCH1 MUTATED PTCH1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 3              86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             9              87
[1] 2 2
[1] FALSE
D12V11, continuous
                 vv
clus               R0  R1  R2  RX
  PTCH1 MUTATED    10   0   0   1
  PTCH1 WILD-TYPE 127  13   2   6
D12V12, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  R0            10             127
  R1             0              13
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED       3                         2     7
  PTCH1 WILD-TYPE    43                         3   107
D12V14, multiclass
                           clus
vv                          PTCH1 MUTATED PTCH1 WILD-TYPE
  ASIAN                                 3              43
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 7             107
[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"
D12V15, binary
                 cls
clus               0  1
  PTCH1 MUTATED    1  3
  PTCH1 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      1    3
  PTCH1 WILD-TYPE    5   85
                        clus
vv                       PTCH1 MUTATED PTCH1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(13) Variable = KIAA2018 MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                  0   1
  KIAA2018 MUTATED     5   8
  KIAA2018 WILD-TYPE 103  69
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                13                172 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 8                 69 
$`KIAA2018 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GI TCGA-2H-A9GR TCGA-IG-A4QS TCGA-KH-A6WC 
        4.31        19.99        14.30        32.45         3.88         6.28 
TCGA-L5-A4OJ TCGA-L5-A8NF TCGA-L5-A8NM TCGA-LN-A49M TCGA-LN-A7HW TCGA-R6-A6Y2 
       21.01         2.66         7.76        12.66        12.00         9.30 
TCGA-R6-A8W8 
        2.89 

$`KIAA2018 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        20.05        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        10.45        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC 
        7.04        38.40         6.35        53.95        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
              2.66               0.13 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
             32.45             122.10 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
               9.3               13.2 
[1] "2.7 - 32.5 (9.3)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2.5"
D13V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA2018 MUTATED         1        1        0        0         3         2
  KIAA2018 WILD-TYPE       7        4        6        1        44        29
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA2018 MUTATED           1          0          1          1        0
  KIAA2018 WILD-TYPE        25         14          8          6        5
                    vv
clus                 STAGE IVA
  KIAA2018 MUTATED           1
  KIAA2018 WILD-TYPE         3
D13V3, multiclass
            clus
vv           KIAA2018 MUTATED KIAA2018 WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  1                  4
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 3                 44
  STAGE IIB                 2                 29
  STAGE III                 1                 25
  STAGE IIIA                0                 14
  STAGE IIIB                1                  8
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  KIAA2018 MUTATED       3  3  5  0
  KIAA2018 WILD-TYPE    29 40 83  5
D13V4, multiclass
       clus
vv      KIAA2018 MUTATED KIAA2018 WILD-TYPE
  T0+T1                3                 29
  T2                   3                 40
  T3                   5                 83
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA2018 MUTATED    7  2  1  1
  KIAA2018 WILD-TYPE 70 67 11  7
D13V5, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  N0                7                 70
  N1                2                 67
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED     8   1
  KIAA2018 WILD-TYPE 128   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      8    1
  KIAA2018 WILD-TYPE  128    8
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0                8                128
  1                1                  8
[1] 2 2
[1] FALSE
D13V7, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED     2  11
  KIAA2018 WILD-TYPE  25 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      2   11
  KIAA2018 WILD-TYPE   25  147
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  FEMALE                2                 25
  MALE                 11                147
[1] 2 2
[1] FALSE
D13V8, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    10   2
  KIAA2018 WILD-TYPE 114  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     10    2
  KIAA2018 WILD-TYPE  114   41
     clus
vv    KIAA2018 MUTATED KIAA2018 WILD-TYPE
  NO                10                114
  YES                2                 41
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    9  4
  KIAA2018 WILD-TYPE 80 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      9    4
  KIAA2018 WILD-TYPE   80   92
                                   clus
vv                                  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    9                 80
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                4                 92
[1] 2 2
[1] FALSE
D13V11, continuous
                    vv
clus                  R0  R1  R2  RX
  KIAA2018 MUTATED     8   1   0   1
  KIAA2018 WILD-TYPE 129  12   2   6
D13V12, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  R0                8                129
  R1                1                 12
  R2                0                  2
  RX                1                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA2018 MUTATED       2                         0     9
  KIAA2018 WILD-TYPE    44                         5   105
D13V14, multiclass
                           clus
vv                          KIAA2018 MUTATED KIAA2018 WILD-TYPE
  ASIAN                                    2                 44
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    9                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    1  5
  KIAA2018 WILD-TYPE  5 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      1    5
  KIAA2018 WILD-TYPE    5   83
                        clus
vv                       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO                5                 83
[1] 2 2
[1] FALSE

Clustering(14) Variable = FAM108A1 MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                  0   1
  FAM108A1 MUTATED     4   0
  FAM108A1 WILD-TYPE 104  77
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 4                181 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 0                 77 
$`FAM108A1 MUTATED`
TCGA-S8-A6BV TCGA-L5-A4OS TCGA-LN-A8HZ TCGA-VR-A8EY 
       20.02        58.59        12.33        33.70 

$`FAM108A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
             12.33               0.13 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
             58.59             122.10 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
             26.86              12.92 
[1] "12.3 - 58.6 (26.9)" "0.1 - 122.1 (12.9)"
[1] "hr="     "2.6e+07"
D14V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM108A1 MUTATED         0        0        0        0         2         1
  FAM108A1 WILD-TYPE       8        5        6        1        45        30
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM108A1 MUTATED           0          1          0          0        0
  FAM108A1 WILD-TYPE        26         13          9          7        5
                    vv
clus                 STAGE IVA
  FAM108A1 MUTATED           0
  FAM108A1 WILD-TYPE         4
D14V3, multiclass
            clus
vv           FAM108A1 MUTATED FAM108A1 WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 2                 45
  STAGE IIB                 1                 30
  STAGE III                 0                 26
  STAGE IIIA                1                 13
  STAGE IIIB                0                  9
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  FAM108A1 MUTATED       0  2  2  0
  FAM108A1 WILD-TYPE    32 41 86  5
D14V4, multiclass
       clus
vv      FAM108A1 MUTATED FAM108A1 WILD-TYPE
  T0+T1                0                 32
  T2                   2                 41
  T3                   2                 86
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  FAM108A1 MUTATED    2  2  0  0
  FAM108A1 WILD-TYPE 75 67 12  8
D14V5, multiclass
    clus
vv   FAM108A1 MUTATED FAM108A1 WILD-TYPE
  N0                2                 75
  N1                2                 67
  N2                0                 12
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     3   0
  FAM108A1 WILD-TYPE 133   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      3    0
  FAM108A1 WILD-TYPE  133    9
   clus
vv  FAM108A1 MUTATED FAM108A1 WILD-TYPE
  0                3                133
  1                0                  9
[1] 2 2
[1] FALSE
D14V7, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     2   2
  FAM108A1 WILD-TYPE  25 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      2    2
  FAM108A1 WILD-TYPE   25  156
        clus
vv       FAM108A1 MUTATED FAM108A1 WILD-TYPE
  FEMALE                2                 25
  MALE                  2                156
[1] 2 2
[1] FALSE
D14V8, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     3   1
  FAM108A1 WILD-TYPE 121  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      3    1
  FAM108A1 WILD-TYPE  121   42
     clus
vv    FAM108A1 MUTATED FAM108A1 WILD-TYPE
  NO                 3                121
  YES                1                 42
[1] 2 2
[1] FALSE
D14V9, continuous
[1] "Remove cluster labels:" "FAM108A1 MUTATED"      
clus
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"FAM108A1 WILD-TYPE" 
D14V10, binary
                    cls
clus                  0  1
  FAM108A1 MUTATED    2  2
  FAM108A1 WILD-TYPE 87 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      2    2
  FAM108A1 WILD-TYPE   87   94
                                   clus
vv                                  FAM108A1 MUTATED FAM108A1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    2                 87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                2                 94
[1] 2 2
[1] FALSE
D14V11, continuous
[1] "Remove cluster labels:" "FAM108A1 MUTATED"      
clus
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U6 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HZ         TCGA-LN-A8I0 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-Z6-AAPN 
"FAM108A1 WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  FAM108A1 MUTATED     4   0   0   0
  FAM108A1 WILD-TYPE 133  13   2   7
D14V12, multiclass
    clus
vv   FAM108A1 MUTATED FAM108A1 WILD-TYPE
  R0                4                133
  R1                0                 13
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM108A1 MUTATED       1                         0     3
  FAM108A1 WILD-TYPE    45                         5   111
D14V14, multiclass
                           clus
vv                          FAM108A1 MUTATED FAM108A1 WILD-TYPE
  ASIAN                                    1                 45
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[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"
D14V15, binary
                    cls
clus                  0  1
  FAM108A1 MUTATED    0  2
  FAM108A1 WILD-TYPE  6 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      0    2
  FAM108A1 WILD-TYPE    6   86
                        clus
vv                       FAM108A1 MUTATED FAM108A1 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                2                 86
[1] 2 2
[1] FALSE

Clustering(15) Variable = PAXIP1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  PAXIP1 MUTATED     6   4
  PAXIP1 WILD-TYPE 102  73
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              10              175 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               4               73 
$`PAXIP1 MUTATED`
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-LN-A49U 
       14.50        68.02        41.52        16.47         8.71        15.35 
TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-VR-A8EO TCGA-VR-A8EU 
        6.35        15.78        25.81        18.31 

$`PAXIP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       38.40        53.95         9.30         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            6.35             0.13 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
           68.02           122.10 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          16.125           12.850 
[1] "6.3 - 68.0 (16.1)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D15V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAXIP1 MUTATED         0        0        0        0         4         0
  PAXIP1 WILD-TYPE       8        5        6        1        43        31
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAXIP1 MUTATED           3          0          0          0        1
  PAXIP1 WILD-TYPE        23         14          9          7        4
                  vv
clus               STAGE IVA
  PAXIP1 MUTATED           1
  PAXIP1 WILD-TYPE         3
D15V3, multiclass
            clus
vv           PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               4               43
  STAGE IIB               0               31
  STAGE III               3               23
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              0                7
  STAGE IV                1                4
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  PAXIP1 MUTATED       1  0  8  0
  PAXIP1 WILD-TYPE    31 43 80  5
D15V4, multiclass
       clus
vv      PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T0+T1              1               31
  T2                 0               43
  T3                 8               80
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PAXIP1 MUTATED    3  5  0  0
  PAXIP1 WILD-TYPE 74 64 12  8
D15V5, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  N0              3               74
  N1              5               64
  N2              0               12
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     7   2
  PAXIP1 WILD-TYPE 129   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      7    2
  PAXIP1 WILD-TYPE  129    7
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0              7              129
  1              2                7
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     2   8
  PAXIP1 WILD-TYPE  25 150
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      2    8
  PAXIP1 WILD-TYPE   25  150
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  FEMALE              2               25
  MALE                8              150
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     6   3
  PAXIP1 WILD-TYPE 118  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      6    3
  PAXIP1 WILD-TYPE  118   40
     clus
vv    PAXIP1 MUTATED PAXIP1 WILD-TYPE
  NO               6              118
  YES              3               40
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    4  6
  PAXIP1 WILD-TYPE 85 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      4    6
  PAXIP1 WILD-TYPE   85   90
                                   clus
vv                                  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  4               85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              6               90
[1] 2 2
[1] FALSE
D15V11, continuous
                  vv
clus                R0  R1  R2  RX
  PAXIP1 MUTATED     8   0   0   0
  PAXIP1 WILD-TYPE 129  13   2   7
D15V12, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  R0              8              129
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAXIP1 MUTATED       3                         0     6
  PAXIP1 WILD-TYPE    43                         5   108
D15V14, multiclass
                           clus
vv                          PAXIP1 MUTATED PAXIP1 WILD-TYPE
  ASIAN                                  3               43
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                  cls
clus                0  1
  PAXIP1 MUTATED    0  4
  PAXIP1 WILD-TYPE  6 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      0    4
  PAXIP1 WILD-TYPE    6   84
                        clus
vv                       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4               84
[1] 2 2
[1] FALSE

Clustering(16) Variable = MGC29506 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  MGC29506 MUTATED     3   1
  MGC29506 WILD-TYPE 105  76
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 4                181 
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 1                 76 
$`MGC29506 MUTATED`
TCGA-JY-A6FD TCGA-JY-A93C TCGA-L5-A8NN TCGA-VR-A8EX 
       68.02        23.18         5.49        28.11 

$`MGC29506 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       44.75         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  MGC29506 MUTATED MGC29506 WILD-TYPE 
              5.49               0.13 
  MGC29506 MUTATED MGC29506 WILD-TYPE 
             68.02             122.10 
  MGC29506 MUTATED MGC29506 WILD-TYPE 
            25.645             12.920 
[1] "5.5 - 68.0 (25.6)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "3.1"
D16V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGC29506 MUTATED         0        0        0        0         1         0
  MGC29506 WILD-TYPE       8        5        6        1        46        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGC29506 MUTATED           1          0          1          0        0
  MGC29506 WILD-TYPE        25         14          8          7        5
                    vv
clus                 STAGE IVA
  MGC29506 MUTATED           1
  MGC29506 WILD-TYPE         3
D16V3, multiclass
            clus
vv           MGC29506 MUTATED MGC29506 WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 1                 46
  STAGE IIB                 0                 31
  STAGE III                 1                 25
  STAGE IIIA                0                 14
  STAGE IIIB                1                  8
  STAGE IIIC                0                  7
  STAGE IV                  0                  5
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  MGC29506 MUTATED       1  0  3  0
  MGC29506 WILD-TYPE    31 43 85  5
D16V4, multiclass
       clus
vv      MGC29506 MUTATED MGC29506 WILD-TYPE
  T0+T1                1                 31
  T2                   0                 43
  T3                   3                 85
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  MGC29506 MUTATED    1  2  1  0
  MGC29506 WILD-TYPE 76 67 11  8
D16V5, multiclass
    clus
vv   MGC29506 MUTATED MGC29506 WILD-TYPE
  N0                1                 76
  N1                2                 67
  N2                1                 11
  N3                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                    cls
clus                   0   1
  MGC29506 MUTATED     3   1
  MGC29506 WILD-TYPE 133   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC29506 MUTATED      3    1
  MGC29506 WILD-TYPE  133    8
   clus
vv  MGC29506 MUTATED MGC29506 WILD-TYPE
  0                3                133
  1                1                  8
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                   0   1
  MGC29506 MUTATED     1   3
  MGC29506 WILD-TYPE  26 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC29506 MUTATED      1    3
  MGC29506 WILD-TYPE   26  155
        clus
vv       MGC29506 MUTATED MGC29506 WILD-TYPE
  FEMALE                1                 26
  MALE                  3                155
[1] 2 2
[1] FALSE
D16V8, binary
                    cls
clus                   0   1
  MGC29506 MUTATED     4   0
  MGC29506 WILD-TYPE 120  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC29506 MUTATED      4    0
  MGC29506 WILD-TYPE  120   43
     clus
vv    MGC29506 MUTATED MGC29506 WILD-TYPE
  NO                 4                120
  YES                0                 43
[1] 2 2
[1] FALSE
D16V9, continuous
[1] "Remove cluster labels:" "MGC29506 MUTATED"      
clus
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-Z6-A8JE 
"MGC29506 WILD-TYPE" 
D16V10, binary
                    cls
clus                  0  1
  MGC29506 MUTATED    2  2
  MGC29506 WILD-TYPE 87 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC29506 MUTATED      2    2
  MGC29506 WILD-TYPE   87   94
                                   clus
vv                                  MGC29506 MUTATED MGC29506 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    2                 87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                2                 94
[1] 2 2
[1] FALSE
D16V11, continuous
[1] "Remove cluster labels:" "MGC29506 MUTATED"      
clus
  MGC29506 MUTATED MGC29506 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NQ 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EZ 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" "MGC29506 WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  MGC29506 MUTATED     4   0   0   0
  MGC29506 WILD-TYPE 133  13   2   7
D16V12, multiclass
    clus
vv   MGC29506 MUTATED MGC29506 WILD-TYPE
  R0                4                133
  R1                0                 13
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MGC29506 MUTATED       2                         0     1
  MGC29506 WILD-TYPE    44                         5   113
D16V14, multiclass
                           clus
vv                          MGC29506 MUTATED MGC29506 WILD-TYPE
  ASIAN                                    2                 44
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    1                113
[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"
D16V15, binary
                    cls
clus                  0  1
  MGC29506 MUTATED    0  0
  MGC29506 WILD-TYPE  6 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC29506 MUTATED      0    0
  MGC29506 WILD-TYPE    6   88

Clustering(17) Variable = C10ORF76 MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  C10ORF76 MUTATED     5   1
  C10ORF76 WILD-TYPE 103  76
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 6                179 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 1                 76 
$`C10ORF76 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3YA TCGA-L5-A43H TCGA-L5-A4OJ TCGA-LN-A8I1 TCGA-VR-AA4G 
       19.99        20.78         0.30        21.01        13.18        18.05 

$`C10ORF76 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
              0.30               0.13 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
             21.01             122.10 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
             19.02              12.85 
[1] "0.3 - 21.0 (19.0)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "2.3"
D17V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C10ORF76 MUTATED         1        0        0        0         1         0
  C10ORF76 WILD-TYPE       7        5        6        1        46        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF76 MUTATED           1          2          0          1        0
  C10ORF76 WILD-TYPE        25         12          9          6        5
                    vv
clus                 STAGE IVA
  C10ORF76 MUTATED           0
  C10ORF76 WILD-TYPE         4
D17V3, multiclass
            clus
vv           C10ORF76 MUTATED C10ORF76 WILD-TYPE
  STAGE I                   1                  7
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 1                 46
  STAGE IIB                 0                 31
  STAGE III                 1                 25
  STAGE IIIA                2                 12
  STAGE IIIB                0                  9
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  C10ORF76 MUTATED       1  2  2  1
  C10ORF76 WILD-TYPE    31 41 86  4
D17V4, multiclass
       clus
vv      C10ORF76 MUTATED C10ORF76 WILD-TYPE
  T0+T1                1                 31
  T2                   2                 41
  T3                   2                 86
  T4                   1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  C10ORF76 MUTATED    3  1  1  1
  C10ORF76 WILD-TYPE 74 68 11  7
D17V5, multiclass
    clus
vv   C10ORF76 MUTATED C10ORF76 WILD-TYPE
  N0                3                 74
  N1                1                 68
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     5   0
  C10ORF76 WILD-TYPE 131   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      5    0
  C10ORF76 WILD-TYPE  131    9
   clus
vv  C10ORF76 MUTATED C10ORF76 WILD-TYPE
  0                5                131
  1                0                  9
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     3   3
  C10ORF76 WILD-TYPE  24 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      3    3
  C10ORF76 WILD-TYPE   24  155
        clus
vv       C10ORF76 MUTATED C10ORF76 WILD-TYPE
  FEMALE                3                 24
  MALE                  3                155
[1] 2 2
[1] FALSE
D17V8, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     5   1
  C10ORF76 WILD-TYPE 119  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      5    1
  C10ORF76 WILD-TYPE  119   42
     clus
vv    C10ORF76 MUTATED C10ORF76 WILD-TYPE
  NO                 5                119
  YES                1                 42
[1] 2 2
[1] FALSE
D17V9, continuous
[1] "Remove cluster labels:" "C10ORF76 MUTATED"      
clus
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A51D 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A7DP         TCGA-KH-A6WC 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA7B         TCGA-VR-AA7D 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
D17V10, binary
                    cls
clus                  0  1
  C10ORF76 MUTATED    2  4
  C10ORF76 WILD-TYPE 87 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      2    4
  C10ORF76 WILD-TYPE   87   92
                                   clus
vv                                  C10ORF76 MUTATED C10ORF76 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    2                 87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                4                 92
[1] 2 2
[1] FALSE
D17V11, continuous
                    vv
clus                  R0  R1  R2  RX
  C10ORF76 MUTATED     5   1   0   0
  C10ORF76 WILD-TYPE 132  12   2   7
D17V12, multiclass
    clus
vv   C10ORF76 MUTATED C10ORF76 WILD-TYPE
  R0                5                132
  R1                1                 12
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C10ORF76 MUTATED       1                         0     5
  C10ORF76 WILD-TYPE    45                         5   109
D17V14, multiclass
                           clus
vv                          C10ORF76 MUTATED C10ORF76 WILD-TYPE
  ASIAN                                    1                 45
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[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"
D17V15, binary
                    cls
clus                  0  1
  C10ORF76 MUTATED    0  2
  C10ORF76 WILD-TYPE  6 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      0    2
  C10ORF76 WILD-TYPE    6   86
                        clus
vv                       C10ORF76 MUTATED C10ORF76 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                2                 86
[1] 2 2
[1] FALSE

Clustering(18) Variable = IPP MUTATION ANALYSIS
D18V1, survival
               sevent
clus2             0   1
  IPP MUTATED     3   3
  IPP WILD-TYPE 105  74
  IPP MUTATED IPP WILD-TYPE 
            6           179 
  IPP MUTATED IPP WILD-TYPE 
            3            74 
$`IPP MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NN 
       14.30         4.21         0.85         7.40        55.50         5.49 

$`IPP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
        7.43        15.48         2.60        25.12         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  IPP MUTATED IPP WILD-TYPE 
         0.85          0.13 
  IPP MUTATED IPP WILD-TYPE 
         55.5         122.1 
  IPP MUTATED IPP WILD-TYPE 
        6.445        13.180 
[1] "0.8 - 55.5 (6.4)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D18V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPP MUTATED         0        0        0        0         1         1
  IPP WILD-TYPE       8        5        6        1        46        30
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPP MUTATED           3          1          0          0        0         0
  IPP WILD-TYPE        23         13          9          7        5         4
D18V3, multiclass
            clus
vv           IPP MUTATED IPP WILD-TYPE
  STAGE I              0             8
  STAGE IA             0             5
  STAGE IB             0             6
  STAGE II             0             1
  STAGE IIA            1            46
  STAGE IIB            1            30
  STAGE III            3            23
  STAGE IIIA           1            13
  STAGE IIIB           0             9
  STAGE IIIC           0             7
  STAGE IV             0             5
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1 T2 T3 T4
  IPP MUTATED       1  1  3  1
  IPP WILD-TYPE    31 42 85  4
D18V4, multiclass
       clus
vv      IPP MUTATED IPP WILD-TYPE
  T0+T1           1            31
  T2              1            42
  T3              3            85
  T4              1             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  IPP MUTATED    1  5  0  0
  IPP WILD-TYPE 76 64 12  8
D18V5, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  N0           1            76
  N1           5            64
  N2           0            12
  N3           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
               cls
clus              0   1
  IPP MUTATED     6   0
  IPP WILD-TYPE 130   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      6    0
  IPP WILD-TYPE  130    9
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0           6           130
  1           0             9
[1] 2 2
[1] FALSE
D18V7, binary
               cls
clus              0   1
  IPP MUTATED     1   5
  IPP WILD-TYPE  26 153
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      1    5
  IPP WILD-TYPE   26  153
        clus
vv       IPP MUTATED IPP WILD-TYPE
  FEMALE           1            26
  MALE             5           153
[1] 2 2
[1] FALSE
D18V8, binary
               cls
clus              0   1
  IPP MUTATED     6   0
  IPP WILD-TYPE 118  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      6    0
  IPP WILD-TYPE  118   43
     clus
vv    IPP MUTATED IPP WILD-TYPE
  NO            6           118
  YES           0            43
[1] 2 2
[1] FALSE
D18V9, continuous
[1] "Remove cluster labels:" "IPP MUTATED"           
clus
  IPP MUTATED IPP WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3YA    TCGA-IG-A3YB    TCGA-IG-A3YC 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC    TCGA-LN-A49K 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O    TCGA-LN-A49P 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"IPP WILD-TYPE" "IPP WILD-TYPE" 
D18V10, binary
               cls
clus             0  1
  IPP MUTATED    4  2
  IPP WILD-TYPE 85 94
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      4    2
  IPP WILD-TYPE   85   94
                                   clus
vv                                  IPP MUTATED IPP WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS               4            85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           2            94
[1] 2 2
[1] FALSE
D18V11, continuous
               vv
clus             R0  R1  R2  RX
  IPP MUTATED     6   0   0   0
  IPP WILD-TYPE 131  13   2   7
D18V12, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  R0           6           131
  R1           0            13
  R2           0             2
  RX           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPP MUTATED       0                         0     4
  IPP WILD-TYPE    46                         5   110
D18V14, multiclass
                           clus
vv                          IPP MUTATED IPP WILD-TYPE
  ASIAN                               0            46
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           110
[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"
D18V15, binary
               cls
clus             0  1
  IPP MUTATED    0  1
  IPP WILD-TYPE  6 87
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      0    1
  IPP WILD-TYPE    6   87
                        clus
vv                       IPP MUTATED IPP WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           1            87
[1] 2 2
[1] FALSE

Clustering(19) Variable = DNAH10 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2               0  1
  DNAH10 MUTATED   12  7
  DNAH10 WILD-TYPE 96 70
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              19              166 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
               7               70 
$`DNAH10 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NT TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4P3 
        4.31        19.99        27.12         7.69         2.63        18.64 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43E 
        0.79         9.96       122.10        44.75        47.38        30.25 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NM TCGA-L5-A8NS 
       26.33        21.01         2.60        55.50         7.76        13.41 
TCGA-LN-A8I0 
       13.38 

$`DNAH10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82         0.36        35.97         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS 
       33.27        35.21         0.85        20.78        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        9.30         0.53        17.03        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.16         0.30        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  DNAH10 MUTATED DNAH10 WILD-TYPE 
            0.79             0.13 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
          122.10            83.24 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
           18.64            12.85 
[1] "0.8 - 122.1 (18.6)" "0.1 - 83.2 (12.8)" 
[1] "hr=" "1.6"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH10 MUTATED         3        0        1        0         1        11
  DNAH10 WILD-TYPE       5        5        5        1        46        20
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH10 MUTATED           1          1          0          1        0
  DNAH10 WILD-TYPE        25         13          9          6        5
                  vv
clus               STAGE IVA
  DNAH10 MUTATED           0
  DNAH10 WILD-TYPE         4
D19V3, multiclass
            clus
vv           DNAH10 MUTATED DNAH10 WILD-TYPE
  STAGE I                 3                5
  STAGE IA                0                5
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               1               46
  STAGE IIB              11               20
  STAGE III               1               25
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  DNAH10 MUTATED       5  7  7  0
  DNAH10 WILD-TYPE    27 36 81  5
D19V4, multiclass
       clus
vv      DNAH10 MUTATED DNAH10 WILD-TYPE
  T0+T1              5               27
  T2                 7               36
  T3                 7               81
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  DNAH10 MUTATED    8 10  0  1
  DNAH10 WILD-TYPE 69 59 12  7
D19V5, multiclass
    clus
vv   DNAH10 MUTATED DNAH10 WILD-TYPE
  N0              8               69
  N1             10               59
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                  cls
clus                 0   1
  DNAH10 MUTATED    15   0
  DNAH10 WILD-TYPE 121   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     15    0
  DNAH10 WILD-TYPE  121    9
   clus
vv  DNAH10 MUTATED DNAH10 WILD-TYPE
  0             15              121
  1              0                9
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  DNAH10 MUTATED     2  17
  DNAH10 WILD-TYPE  25 141
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED      2   17
  DNAH10 WILD-TYPE   25  141
        clus
vv       DNAH10 MUTATED DNAH10 WILD-TYPE
  FEMALE              2               25
  MALE               17              141
[1] 2 2
[1] FALSE
D19V8, binary
                  cls
clus                 0   1
  DNAH10 MUTATED    14   4
  DNAH10 WILD-TYPE 110  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     14    4
  DNAH10 WILD-TYPE  110   39
     clus
vv    DNAH10 MUTATED DNAH10 WILD-TYPE
  NO              14              110
  YES              4               39
[1] 2 2
[1] FALSE
D19V9, continuous
[1] "Remove cluster labels:" "DNAH10 MUTATED"        
clus
  DNAH10 MUTATED DNAH10 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
D19V10, binary
                  cls
clus                0  1
  DNAH10 MUTATED   12  7
  DNAH10 WILD-TYPE 77 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     12    7
  DNAH10 WILD-TYPE   77   89
                                   clus
vv                                  DNAH10 MUTATED DNAH10 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 12               77
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              7               89
[1] 2 2
[1] FALSE
D19V11, continuous
                  vv
clus                R0  R1  R2  RX
  DNAH10 MUTATED    16   1   0   1
  DNAH10 WILD-TYPE 121  12   2   6
D19V12, multiclass
    clus
vv   DNAH10 MUTATED DNAH10 WILD-TYPE
  R0             16              121
  R1              1               12
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH10 MUTATED       2                         0    17
  DNAH10 WILD-TYPE    44                         5    97
D19V14, multiclass
                           clus
vv                          DNAH10 MUTATED DNAH10 WILD-TYPE
  ASIAN                                  2               44
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 17               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                  cls
clus                0  1
  DNAH10 MUTATED    0  6
  DNAH10 WILD-TYPE  6 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED      0    6
  DNAH10 WILD-TYPE    6   82
                        clus
vv                       DNAH10 MUTATED DNAH10 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6               82
[1] 2 2
[1] FALSE

Clustering(20) Variable = RIC3 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  RIC3 MUTATED     2   2
  RIC3 WILD-TYPE 106  75
  RIC3 MUTATED RIC3 WILD-TYPE 
             4            181 
  RIC3 MUTATED RIC3 WILD-TYPE 
             2             75 
$`RIC3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NM TCGA-L5-A8NS 
        4.31        19.99         7.76        13.41 

$`RIC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  RIC3 MUTATED RIC3 WILD-TYPE 
          4.31           0.13 
  RIC3 MUTATED RIC3 WILD-TYPE 
         19.99         122.10 
  RIC3 MUTATED RIC3 WILD-TYPE 
        10.585         13.150 
[1] "4.3 - 20.0 (10.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.9"
D20V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RIC3 MUTATED         0        0        0        0         0         3
  RIC3 WILD-TYPE       8        5        6        1        47        28
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIC3 MUTATED           0          0          0          1        0         0
  RIC3 WILD-TYPE        26         14          9          6        5         4
D20V3, multiclass
            clus
vv           RIC3 MUTATED RIC3 WILD-TYPE
  STAGE I               0              8
  STAGE IA              0              5
  STAGE IB              0              6
  STAGE II              0              1
  STAGE IIA             0             47
  STAGE IIB             3             28
  STAGE III             0             26
  STAGE IIIA            0             14
  STAGE IIIB            0              9
  STAGE IIIC            1              6
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  RIC3 MUTATED       0  1  3  0
  RIC3 WILD-TYPE    32 42 85  5
D20V4, multiclass
       clus
vv      RIC3 MUTATED RIC3 WILD-TYPE
  T0+T1            0             32
  T2               1             42
  T3               3             85
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RIC3 MUTATED    2  1  0  1
  RIC3 WILD-TYPE 75 68 12  7
D20V5, multiclass
    clus
vv   RIC3 MUTATED RIC3 WILD-TYPE
  N0            2             75
  N1            1             68
  N2            0             12
  N3            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                cls
clus               0   1
  RIC3 MUTATED     2   0
  RIC3 WILD-TYPE 134   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      2    0
  RIC3 WILD-TYPE  134    9
   clus
vv  RIC3 MUTATED RIC3 WILD-TYPE
  0            2            134
  1            0              9
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  RIC3 MUTATED     1   3
  RIC3 WILD-TYPE  26 155
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      1    3
  RIC3 WILD-TYPE   26  155
        clus
vv       RIC3 MUTATED RIC3 WILD-TYPE
  FEMALE            1             26
  MALE              3            155
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  RIC3 MUTATED     2   1
  RIC3 WILD-TYPE 122  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      2    1
  RIC3 WILD-TYPE  122   42
     clus
vv    RIC3 MUTATED RIC3 WILD-TYPE
  NO             2            122
  YES            1             42
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, binary
                cls
clus              0  1
  RIC3 MUTATED    3  1
  RIC3 WILD-TYPE 86 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      3    1
  RIC3 WILD-TYPE   86   95
                                   clus
vv                                  RIC3 MUTATED RIC3 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                3             86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            1             95
[1] 2 2
[1] FALSE
D20V11, continuous
                vv
clus              R0  R1  R2  RX
  RIC3 MUTATED     3   0   0   1
  RIC3 WILD-TYPE 134  13   2   6
D20V12, multiclass
    clus
vv   RIC3 MUTATED RIC3 WILD-TYPE
  R0            3            134
  R1            0             13
  R2            0              2
  RX            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIC3 MUTATED       0                         0     4
  RIC3 WILD-TYPE    46                         5   110
D20V14, multiclass
                           clus
vv                          RIC3 MUTATED RIC3 WILD-TYPE
  ASIAN                                0             46
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[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"
D20V15, binary
                cls
clus              0  1
  RIC3 MUTATED    0  0
  RIC3 WILD-TYPE  6 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      0    0
  RIC3 WILD-TYPE    6   88

Clustering(21) Variable = HMMR MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  HMMR MUTATED     2   2
  HMMR WILD-TYPE 106  75
  HMMR MUTATED HMMR WILD-TYPE 
             4            181 
  HMMR MUTATED HMMR WILD-TYPE 
             2             75 
$`HMMR MUTATED`
TCGA-2H-A9GF TCGA-JY-A6FG TCGA-L5-A4OH TCGA-LN-A49X 
       25.78        41.52        32.61        12.62 

$`HMMR WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12         5.16        20.02        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  HMMR MUTATED HMMR WILD-TYPE 
         12.62           0.13 
  HMMR MUTATED HMMR WILD-TYPE 
         41.52         122.10 
  HMMR MUTATED HMMR WILD-TYPE 
        29.195         12.920 
[1] "12.6 - 41.5 (29.2)" "0.1 - 122.1 (12.9)"
[1] "hr=" "1.4"
D21V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HMMR MUTATED         1        0        0        0         1         0
  HMMR WILD-TYPE       7        5        6        1        46        31
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMMR MUTATED           2          0          0          0        0         0
  HMMR WILD-TYPE        24         14          9          7        5         4
D21V3, multiclass
            clus
vv           HMMR MUTATED HMMR WILD-TYPE
  STAGE I               1              7
  STAGE IA              0              5
  STAGE IB              0              6
  STAGE II              0              1
  STAGE IIA             1             46
  STAGE IIB             0             31
  STAGE III             2             24
  STAGE IIIA            0             14
  STAGE IIIB            0              9
  STAGE IIIC            0              7
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  HMMR MUTATED       1  0  3  0
  HMMR WILD-TYPE    31 43 85  5
D21V4, multiclass
       clus
vv      HMMR MUTATED HMMR WILD-TYPE
  T0+T1            1             31
  T2               0             43
  T3               3             85
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  HMMR MUTATED    2  2  0  0
  HMMR WILD-TYPE 75 67 12  8
D21V5, multiclass
    clus
vv   HMMR MUTATED HMMR WILD-TYPE
  N0            2             75
  N1            2             67
  N2            0             12
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  HMMR MUTATED     4   0
  HMMR WILD-TYPE 132   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      4    0
  HMMR WILD-TYPE  132    9
   clus
vv  HMMR MUTATED HMMR WILD-TYPE
  0            4            132
  1            0              9
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  HMMR MUTATED     0   4
  HMMR WILD-TYPE  27 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      0    4
  HMMR WILD-TYPE   27  154
        clus
vv       HMMR MUTATED HMMR WILD-TYPE
  FEMALE            0             27
  MALE              4            154
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus               0   1
  HMMR MUTATED     3   1
  HMMR WILD-TYPE 121  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      3    1
  HMMR WILD-TYPE  121   42
     clus
vv    HMMR MUTATED HMMR WILD-TYPE
  NO             3            121
  YES            1             42
[1] 2 2
[1] FALSE
D21V9, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
D21V10, binary
                cls
clus              0  1
  HMMR MUTATED    2  2
  HMMR WILD-TYPE 87 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      2    2
  HMMR WILD-TYPE   87   94
                                   clus
vv                                  HMMR MUTATED HMMR WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                2             87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            2             94
[1] 2 2
[1] FALSE
D21V11, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OM     TCGA-L5-A4ON 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  HMMR MUTATED     3   1   0   0
  HMMR WILD-TYPE 134  12   2   7
D21V12, multiclass
    clus
vv   HMMR MUTATED HMMR WILD-TYPE
  R0            3            134
  R1            1             12
  R2            0              2
  RX            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMMR MUTATED       1                         0     2
  HMMR WILD-TYPE    45                         5   112
D21V14, multiclass
                           clus
vv                          HMMR MUTATED HMMR WILD-TYPE
  ASIAN                                1             45
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            112
[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"
D21V15, binary
                cls
clus              0  1
  HMMR MUTATED    0  1
  HMMR WILD-TYPE  6 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      0    1
  HMMR WILD-TYPE    6   87
                        clus
vv                       HMMR MUTATED HMMR WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            1             87
[1] 2 2
[1] FALSE

Clustering(22) Variable = PIAS1 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  PIAS1 MUTATED     3   2
  PIAS1 WILD-TYPE 105  75
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              5             180 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              2              75 
$`PIAS1 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GI TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-L5-A4OH 
       19.99        14.30        20.78        18.64        32.61 

$`PIAS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ 
        5.16        20.02        25.78        20.05        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  PIAS1 MUTATED PIAS1 WILD-TYPE 
          14.30            0.13 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
          32.61          122.10 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
          19.99           12.85 
[1] "14.3 - 32.6 (20.0)" "0.1 - 122.1 (12.8)"
[1] "hr=" "1.4"
D22V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIAS1 MUTATED         1        0        0        0         0         1
  PIAS1 WILD-TYPE       7        5        6        1        47        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIAS1 MUTATED           1          1          0          1        0         0
  PIAS1 WILD-TYPE        25         13          9          6        5         4
D22V3, multiclass
            clus
vv           PIAS1 MUTATED PIAS1 WILD-TYPE
  STAGE I                1               7
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              0              47
  STAGE IIB              1              30
  STAGE III              1              25
  STAGE IIIA             1              13
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  PIAS1 MUTATED       1  1  2  1
  PIAS1 WILD-TYPE    31 42 86  4
D22V4, multiclass
       clus
vv      PIAS1 MUTATED PIAS1 WILD-TYPE
  T0+T1             1              31
  T2                1              42
  T3                2              86
  T4                1               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PIAS1 MUTATED    2  2  0  1
  PIAS1 WILD-TYPE 75 67 12  7
D22V5, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  N0             2              75
  N1             2              67
  N2             0              12
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                 cls
clus                0   1
  PIAS1 MUTATED     4   0
  PIAS1 WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      4    0
  PIAS1 WILD-TYPE  132    9
   clus
vv  PIAS1 MUTATED PIAS1 WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  PIAS1 MUTATED     0   5
  PIAS1 WILD-TYPE  27 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      0    5
  PIAS1 WILD-TYPE   27  153
        clus
vv       PIAS1 MUTATED PIAS1 WILD-TYPE
  FEMALE             0              27
  MALE               5             153
[1] 2 2
[1] FALSE
D22V8, binary
                 cls
clus                0   1
  PIAS1 MUTATED     4   1
  PIAS1 WILD-TYPE 120  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      4    1
  PIAS1 WILD-TYPE  120   42
     clus
vv    PIAS1 MUTATED PIAS1 WILD-TYPE
  NO              4             120
  YES             1              42
[1] 2 2
[1] FALSE
D22V9, continuous
[1] "Remove cluster labels:" "PIAS1 MUTATED"         
clus
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YB 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
D22V10, binary
                 cls
clus               0  1
  PIAS1 MUTATED    3  2
  PIAS1 WILD-TYPE 86 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      3    2
  PIAS1 WILD-TYPE   86   94
                                   clus
vv                                  PIAS1 MUTATED PIAS1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 3              86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D22V11, continuous
                 vv
clus               R0  R1  R2  RX
  PIAS1 MUTATED     5   0   0   0
  PIAS1 WILD-TYPE 132  13   2   7
D22V12, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  R0             5             132
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIAS1 MUTATED       0                         0     4
  PIAS1 WILD-TYPE    46                         5   110
D22V14, multiclass
                           clus
vv                          PIAS1 MUTATED PIAS1 WILD-TYPE
  ASIAN                                 0              46
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[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"
D22V15, binary
                 cls
clus               0  1
  PIAS1 MUTATED    0  2
  PIAS1 WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      0    2
  PIAS1 WILD-TYPE    6   86
                        clus
vv                       PIAS1 MUTATED PIAS1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(23) Variable = ITGA6 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  ITGA6 MUTATED     4   3
  ITGA6 WILD-TYPE 104  74
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              7             178 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              74 
$`ITGA6 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-2H-A9GI TCGA-L5-A8NM TCGA-LN-A49P TCGA-LN-A5U6 
        4.31        27.12        14.30         7.76        12.33        12.33 
TCGA-LN-A7HX 
       12.23 

$`ITGA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.02        25.78        20.05        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  ITGA6 MUTATED ITGA6 WILD-TYPE 
           4.31            0.13 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          27.12          122.10 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          12.33           13.18 
[1] "4.3 - 27.1 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.4"
D23V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGA6 MUTATED         0        0        0        0         2         4
  ITGA6 WILD-TYPE       8        5        6        1        45        27
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA6 MUTATED           1          0          0          0        0         0
  ITGA6 WILD-TYPE        25         14          9          7        5         4
D23V3, multiclass
            clus
vv           ITGA6 MUTATED ITGA6 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              2              45
  STAGE IIB              4              27
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  ITGA6 MUTATED       0  3  4  0
  ITGA6 WILD-TYPE    32 40 84  5
D23V4, multiclass
       clus
vv      ITGA6 MUTATED ITGA6 WILD-TYPE
  T0+T1             0              32
  T2                3              40
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ITGA6 MUTATED    4  3  0  0
  ITGA6 WILD-TYPE 73 66 12  8
D23V5, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  N0             4              73
  N1             3              66
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                 cls
clus                0   1
  ITGA6 MUTATED     6   0
  ITGA6 WILD-TYPE 130   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      6    0
  ITGA6 WILD-TYPE  130    9
   clus
vv  ITGA6 MUTATED ITGA6 WILD-TYPE
  0             6             130
  1             0               9
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  ITGA6 MUTATED     1   6
  ITGA6 WILD-TYPE  26 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      1    6
  ITGA6 WILD-TYPE   26  152
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  FEMALE             1              26
  MALE               6             152
[1] 2 2
[1] FALSE
D23V8, binary
                 cls
clus                0   1
  ITGA6 MUTATED     2   4
  ITGA6 WILD-TYPE 122  39
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      2    4
  ITGA6 WILD-TYPE  122   39
     clus
vv    ITGA6 MUTATED ITGA6 WILD-TYPE
  NO              2             122
  YES             4              39
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, binary
                 cls
clus               0  1
  ITGA6 MUTATED    3  4
  ITGA6 WILD-TYPE 86 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      3    4
  ITGA6 WILD-TYPE   86   92
                                   clus
vv                                  ITGA6 MUTATED ITGA6 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 3              86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             4              92
[1] 2 2
[1] FALSE
D23V11, continuous
                 vv
clus               R0  R1  R2  RX
  ITGA6 MUTATED     5   1   0   1
  ITGA6 WILD-TYPE 132  12   2   6
D23V12, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  R0             5             132
  R1             1              12
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGA6 MUTATED       3                         0     3
  ITGA6 WILD-TYPE    43                         5   111
D23V14, multiclass
                           clus
vv                          ITGA6 MUTATED ITGA6 WILD-TYPE
  ASIAN                                 3              43
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[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"
D23V15, binary
                 cls
clus               0  1
  ITGA6 MUTATED    0  3
  ITGA6 WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    3
  ITGA6 WILD-TYPE    6   85
                        clus
vv                       ITGA6 MUTATED ITGA6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(24) Variable = ASTE1 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  ASTE1 MUTATED     5   0
  ASTE1 WILD-TYPE 103  77
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              5             180 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              0              77 
$`ASTE1 MUTATED`
TCGA-L5-A4OG TCGA-JY-A939 TCGA-L5-A4OO TCGA-L5-A8NR TCGA-Q9-A6FW 
        4.70        21.70         3.32         8.71         7.82 

$`ASTE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  ASTE1 MUTATED ASTE1 WILD-TYPE 
           3.32            0.13 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
           21.7           122.1 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
           7.82           13.18 
[1] "3.3 - 21.7 (7.8)"   "0.1 - 122.1 (13.2)"
[1] "hr="     "9200000"
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASTE1 MUTATED         1        0        0        0         0         1
  ASTE1 WILD-TYPE       7        5        6        1        47        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASTE1 MUTATED           1          0          1          1        0         0
  ASTE1 WILD-TYPE        25         14          8          6        5         4
D24V3, multiclass
            clus
vv           ASTE1 MUTATED ASTE1 WILD-TYPE
  STAGE I                1               7
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              0              47
  STAGE IIB              1              30
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             1               8
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  ASTE1 MUTATED       2  0  3  0
  ASTE1 WILD-TYPE    30 43 85  5
D24V4, multiclass
       clus
vv      ASTE1 MUTATED ASTE1 WILD-TYPE
  T0+T1             2              30
  T2                0              43
  T3                3              85
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ASTE1 MUTATED    1  2  1  1
  ASTE1 WILD-TYPE 76 67 11  7
D24V5, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  N0             1              76
  N1             2              67
  N2             1              11
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                 cls
clus                0   1
  ASTE1 MUTATED     5   0
  ASTE1 WILD-TYPE 131   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      5    0
  ASTE1 WILD-TYPE  131    9
   clus
vv  ASTE1 MUTATED ASTE1 WILD-TYPE
  0             5             131
  1             0               9
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  ASTE1 MUTATED     2   3
  ASTE1 WILD-TYPE  25 155
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      2    3
  ASTE1 WILD-TYPE   25  155
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  FEMALE             2              25
  MALE               3             155
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus                0   1
  ASTE1 MUTATED     4   0
  ASTE1 WILD-TYPE 120  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      4    0
  ASTE1 WILD-TYPE  120   43
     clus
vv    ASTE1 MUTATED ASTE1 WILD-TYPE
  NO              4             120
  YES             0              43
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, binary
                 cls
clus               0  1
  ASTE1 MUTATED    5  0
  ASTE1 WILD-TYPE 84 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      5    0
  ASTE1 WILD-TYPE   84   96
                                   clus
vv                                  ASTE1 MUTATED ASTE1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 5              84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             0              96
[1] 2 2
[1] FALSE
D24V11, continuous
                 vv
clus               R0  R1  R2  RX
  ASTE1 MUTATED     4   0   0   1
  ASTE1 WILD-TYPE 133  13   2   6
D24V12, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  R0             4             133
  R1             0              13
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASTE1 MUTATED       0                         0     4
  ASTE1 WILD-TYPE    46                         5   110
D24V14, multiclass
                           clus
vv                          ASTE1 MUTATED ASTE1 WILD-TYPE
  ASIAN                                 0              46
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[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"
D24V15, binary
                 cls
clus               0  1
  ASTE1 MUTATED    0  1
  ASTE1 WILD-TYPE  6 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      0    1
  ASTE1 WILD-TYPE    6   87
                        clus
vv                       ASTE1 MUTATED ASTE1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             1              87
[1] 2 2
[1] FALSE

Clustering(25) Variable = KPNA1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  KPNA1 MUTATED     2   4
  KPNA1 WILD-TYPE 106  73
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             179 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              4              73 
$`KPNA1 MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A4P3 TCGA-JY-A93D TCGA-L5-A4OH TCGA-LN-A8I0 
        5.92         4.21        18.64        31.56        32.61        13.38 

$`KPNA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  KPNA1 MUTATED KPNA1 WILD-TYPE 
           4.21            0.13 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
          32.61          122.10 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
          16.01           12.92 
[1] "4.2 - 32.6 (16.0)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "1.5"
D25V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KPNA1 MUTATED         1        0        0        0         1         1
  KPNA1 WILD-TYPE       7        5        6        1        46        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNA1 MUTATED           2          0          0          1        0         0
  KPNA1 WILD-TYPE        24         14          9          6        5         4
D25V3, multiclass
            clus
vv           KPNA1 MUTATED KPNA1 WILD-TYPE
  STAGE I                1               7
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              1              30
  STAGE III              2              24
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  KPNA1 MUTATED       1  3  2  0
  KPNA1 WILD-TYPE    31 40 86  5
D25V4, multiclass
       clus
vv      KPNA1 MUTATED KPNA1 WILD-TYPE
  T0+T1             1              31
  T2                3              40
  T3                2              86
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KPNA1 MUTATED    2  3  0  1
  KPNA1 WILD-TYPE 75 66 12  7
D25V5, multiclass
    clus
vv   KPNA1 MUTATED KPNA1 WILD-TYPE
  N0             2              75
  N1             3              66
  N2             0              12
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                 cls
clus                0   1
  KPNA1 MUTATED     6   0
  KPNA1 WILD-TYPE 130   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      6    0
  KPNA1 WILD-TYPE  130    9
   clus
vv  KPNA1 MUTATED KPNA1 WILD-TYPE
  0             6             130
  1             0               9
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  KPNA1 MUTATED     0   6
  KPNA1 WILD-TYPE  27 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      0    6
  KPNA1 WILD-TYPE   27  152
        clus
vv       KPNA1 MUTATED KPNA1 WILD-TYPE
  FEMALE             0              27
  MALE               6             152
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  KPNA1 MUTATED     4   2
  KPNA1 WILD-TYPE 120  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      4    2
  KPNA1 WILD-TYPE  120   41
     clus
vv    KPNA1 MUTATED KPNA1 WILD-TYPE
  NO              4             120
  YES             2              41
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, binary
                 cls
clus               0  1
  KPNA1 MUTATED    4  2
  KPNA1 WILD-TYPE 85 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      4    2
  KPNA1 WILD-TYPE   85   94
                                   clus
vv                                  KPNA1 MUTATED KPNA1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 4              85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D25V11, continuous
                 vv
clus               R0  R1  R2  RX
  KPNA1 MUTATED     5   1   0   0
  KPNA1 WILD-TYPE 132  12   2   7
D25V12, multiclass
    clus
vv   KPNA1 MUTATED KPNA1 WILD-TYPE
  R0             5             132
  R1             1              12
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KPNA1 MUTATED       1                         0     3
  KPNA1 WILD-TYPE    45                         5   111
D25V14, multiclass
                           clus
vv                          KPNA1 MUTATED KPNA1 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[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"
D25V15, binary
                 cls
clus               0  1
  KPNA1 MUTATED    0  2
  KPNA1 WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      0    2
  KPNA1 WILD-TYPE    6   86
                        clus
vv                       KPNA1 MUTATED KPNA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(26) Variable = LIMA1 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  LIMA1 MUTATED     4   4
  LIMA1 WILD-TYPE 104  73
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              8             177 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
              4              73 
$`LIMA1 MUTATED`
TCGA-JY-A6FB TCGA-IG-A4P3 TCGA-L5-A4OH TCGA-L5-A4OS TCGA-L5-A8NF TCGA-L5-A8NM 
       60.39        18.64        32.61        58.59         2.66         7.76 
TCGA-LN-A9FQ TCGA-RE-A7BO 
       12.85         7.00 

$`LIMA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  LIMA1 MUTATED LIMA1 WILD-TYPE 
           2.66            0.13 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
          60.39          122.10 
  LIMA1 MUTATED LIMA1 WILD-TYPE 
         15.745          13.150 
[1] "2.7 - 60.4 (15.7)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D26V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LIMA1 MUTATED         2        0        0        0         1         4
  LIMA1 WILD-TYPE       6        5        6        1        46        27
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIMA1 MUTATED           0          0          0          0        0         1
  LIMA1 WILD-TYPE        26         14          9          7        5         3
D26V3, multiclass
            clus
vv           LIMA1 MUTATED LIMA1 WILD-TYPE
  STAGE I                2               6
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              4              27
  STAGE III              0              26
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  LIMA1 MUTATED       4  3  1  0
  LIMA1 WILD-TYPE    28 40 87  5
D26V4, multiclass
       clus
vv      LIMA1 MUTATED LIMA1 WILD-TYPE
  T0+T1             4              28
  T2                3              40
  T3                1              87
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LIMA1 MUTATED    4  4  0  0
  LIMA1 WILD-TYPE 73 65 12  8
D26V5, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  N0             4              73
  N1             4              65
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                 cls
clus                0   1
  LIMA1 MUTATED     7   1
  LIMA1 WILD-TYPE 129   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      7    1
  LIMA1 WILD-TYPE  129    8
   clus
vv  LIMA1 MUTATED LIMA1 WILD-TYPE
  0             7             129
  1             1               8
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  LIMA1 MUTATED     3   5
  LIMA1 WILD-TYPE  24 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      3    5
  LIMA1 WILD-TYPE   24  153
        clus
vv       LIMA1 MUTATED LIMA1 WILD-TYPE
  FEMALE             3              24
  MALE               5             153
[1] 2 2
[1] FALSE
D26V8, binary
                 cls
clus                0   1
  LIMA1 MUTATED     7   1
  LIMA1 WILD-TYPE 117  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      7    1
  LIMA1 WILD-TYPE  117   42
     clus
vv    LIMA1 MUTATED LIMA1 WILD-TYPE
  NO              7             117
  YES             1              42
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, binary
                 cls
clus               0  1
  LIMA1 MUTATED    6  2
  LIMA1 WILD-TYPE 83 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      6    2
  LIMA1 WILD-TYPE   83   94
                                   clus
vv                                  LIMA1 MUTATED LIMA1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 6              83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D26V11, continuous
                 vv
clus               R0  R1  R2  RX
  LIMA1 MUTATED     8   0   0   0
  LIMA1 WILD-TYPE 129  13   2   7
D26V12, multiclass
    clus
vv   LIMA1 MUTATED LIMA1 WILD-TYPE
  R0             8             129
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIMA1 MUTATED       1                         0     7
  LIMA1 WILD-TYPE    45                         5   107
D26V14, multiclass
                           clus
vv                          LIMA1 MUTATED LIMA1 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[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"
D26V15, binary
                 cls
clus               0  1
  LIMA1 MUTATED    0  3
  LIMA1 WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMA1 MUTATED      0    3
  LIMA1 WILD-TYPE    6   85
                        clus
vv                       LIMA1 MUTATED LIMA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(27) Variable = FAM65B MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  FAM65B MUTATED     5   3
  FAM65B WILD-TYPE 103  74
  FAM65B MUTATED FAM65B WILD-TYPE 
               8              177 
  FAM65B MUTATED FAM65B WILD-TYPE 
               3               74 
$`FAM65B MUTATED`
TCGA-IC-A6RE TCGA-JY-A6FG TCGA-L5-A4OM TCGA-L5-A4OU TCGA-L5-A8NH TCGA-LN-A49Y 
        7.69        41.52        47.93        29.00        12.92        12.46 
TCGA-LN-A5U7 TCGA-Z6-A9VB 
       25.25         1.32 

$`FAM65B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         2.66        19.73 

  FAM65B MUTATED FAM65B WILD-TYPE 
            1.32             0.13 
  FAM65B MUTATED FAM65B WILD-TYPE 
           47.93           122.10 
  FAM65B MUTATED FAM65B WILD-TYPE 
          19.085           13.150 
[1] "1.3 - 47.9 (19.1)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D27V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM65B MUTATED         0        1        0        0         3         1
  FAM65B WILD-TYPE       8        4        6        1        44        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM65B MUTATED           1          1          0          0        1
  FAM65B WILD-TYPE        25         13          9          7        4
                  vv
clus               STAGE IVA
  FAM65B MUTATED           0
  FAM65B WILD-TYPE         4
D27V3, multiclass
            clus
vv           FAM65B MUTATED FAM65B WILD-TYPE
  STAGE I                 0                8
  STAGE IA                1                4
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               3               44
  STAGE IIB               1               30
  STAGE III               1               25
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              0                7
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  FAM65B MUTATED       3  1  4  0
  FAM65B WILD-TYPE    29 42 84  5
D27V4, multiclass
       clus
vv      FAM65B MUTATED FAM65B WILD-TYPE
  T0+T1              3               29
  T2                 1               42
  T3                 4               84
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  FAM65B MUTATED    5  3  0  0
  FAM65B WILD-TYPE 72 66 12  8
D27V5, multiclass
    clus
vv   FAM65B MUTATED FAM65B WILD-TYPE
  N0              5               72
  N1              3               66
  N2              0               12
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                  cls
clus                 0   1
  FAM65B MUTATED     6   1
  FAM65B WILD-TYPE 130   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      6    1
  FAM65B WILD-TYPE  130    8
   clus
vv  FAM65B MUTATED FAM65B WILD-TYPE
  0              6              130
  1              1                8
[1] 2 2
[1] FALSE
D27V7, binary
                  cls
clus                 0   1
  FAM65B MUTATED     1   7
  FAM65B WILD-TYPE  26 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      1    7
  FAM65B WILD-TYPE   26  151
        clus
vv       FAM65B MUTATED FAM65B WILD-TYPE
  FEMALE              1               26
  MALE                7              151
[1] 2 2
[1] FALSE
D27V8, binary
                  cls
clus                 0   1
  FAM65B MUTATED     7   0
  FAM65B WILD-TYPE 117  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      7    0
  FAM65B WILD-TYPE  117   43
     clus
vv    FAM65B MUTATED FAM65B WILD-TYPE
  NO               7              117
  YES              0               43
[1] 2 2
[1] FALSE
D27V9, continuous
[1] "Remove cluster labels:" "FAM65B MUTATED"        
clus
  FAM65B MUTATED FAM65B WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A7HV       TCGA-LN-A7HW 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FAM65B WILD-TYPE" "FAM65B WILD-TYPE" 
D27V10, binary
                  cls
clus                0  1
  FAM65B MUTATED    3  5
  FAM65B WILD-TYPE 86 91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      3    5
  FAM65B WILD-TYPE   86   91
                                   clus
vv                                  FAM65B MUTATED FAM65B WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  3               86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              5               91
[1] 2 2
[1] FALSE
D27V11, continuous
                  vv
clus                R0  R1  R2  RX
  FAM65B MUTATED     8   0   0   0
  FAM65B WILD-TYPE 129  13   2   7
D27V12, multiclass
    clus
vv   FAM65B MUTATED FAM65B WILD-TYPE
  R0              8              129
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM65B MUTATED       2                         0     6
  FAM65B WILD-TYPE    44                         5   108
D27V14, multiclass
                           clus
vv                          FAM65B MUTATED FAM65B WILD-TYPE
  ASIAN                                  2               44
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                  cls
clus                0  1
  FAM65B MUTATED    0  4
  FAM65B WILD-TYPE  6 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65B MUTATED      0    4
  FAM65B WILD-TYPE    6   84
                        clus
vv                       FAM65B MUTATED FAM65B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4               84
[1] 2 2
[1] FALSE

Clustering(28) Variable = CORO7 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  CORO7 MUTATED     7   0
  CORO7 WILD-TYPE 101  77
  CORO7 MUTATED CORO7 WILD-TYPE 
              7             178 
  CORO7 MUTATED CORO7 WILD-TYPE 
              0              77 
$`CORO7 MUTATED`
TCGA-L5-A43M TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-L5-A43C TCGA-L5-A891 TCGA-L5-A8NK 
        8.94         7.69       122.10         3.16         3.75        13.55 
TCGA-Z6-A8JE 
        2.10 

$`CORO7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         1.32         2.66        19.73 

  CORO7 MUTATED CORO7 WILD-TYPE 
           2.10            0.13 
  CORO7 MUTATED CORO7 WILD-TYPE 
         122.10           83.24 
  CORO7 MUTATED CORO7 WILD-TYPE 
           7.69           13.18 
[1] "2.1 - 122.1 (7.7)" "0.1 - 83.2 (13.2)"
[1] "hr="     "3.2e+07"
D28V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CORO7 MUTATED         1        0        0        0         1         1
  CORO7 WILD-TYPE       7        5        6        1        46        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CORO7 MUTATED           0          1          0          0        0         0
  CORO7 WILD-TYPE        26         13          9          7        5         4
D28V3, multiclass
            clus
vv           CORO7 MUTATED CORO7 WILD-TYPE
  STAGE I                1               7
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              1              30
  STAGE III              0              26
  STAGE IIIA             1              13
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  CORO7 MUTATED       2  0  4  0
  CORO7 WILD-TYPE    30 43 84  5
D28V4, multiclass
       clus
vv      CORO7 MUTATED CORO7 WILD-TYPE
  T0+T1             2              30
  T2                0              43
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CORO7 MUTATED    2  3  1  0
  CORO7 WILD-TYPE 75 66 11  8
D28V5, multiclass
    clus
vv   CORO7 MUTATED CORO7 WILD-TYPE
  N0             2              75
  N1             3              66
  N2             1              11
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                 cls
clus                0   1
  CORO7 MUTATED     5   0
  CORO7 WILD-TYPE 131   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORO7 MUTATED      5    0
  CORO7 WILD-TYPE  131    9
   clus
vv  CORO7 MUTATED CORO7 WILD-TYPE
  0             5             131
  1             0               9
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus                0   1
  CORO7 MUTATED     2   5
  CORO7 WILD-TYPE  25 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORO7 MUTATED      2    5
  CORO7 WILD-TYPE   25  153
        clus
vv       CORO7 MUTATED CORO7 WILD-TYPE
  FEMALE             2              25
  MALE               5             153
[1] 2 2
[1] FALSE
D28V8, binary
                 cls
clus                0   1
  CORO7 MUTATED     5   0
  CORO7 WILD-TYPE 119  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORO7 MUTATED      5    0
  CORO7 WILD-TYPE  119   43
     clus
vv    CORO7 MUTATED CORO7 WILD-TYPE
  NO              5             119
  YES             0              43
[1] 2 2
[1] FALSE
D28V9, continuous
[1] "Remove cluster labels:" "CORO7 MUTATED"         
clus
  CORO7 MUTATED CORO7 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JD 
"CORO7 WILD-TYPE" "CORO7 WILD-TYPE" "CORO7 WILD-TYPE" 
D28V10, binary
                 cls
clus               0  1
  CORO7 MUTATED    5  2
  CORO7 WILD-TYPE 84 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORO7 MUTATED      5    2
  CORO7 WILD-TYPE   84   94
                                   clus
vv                                  CORO7 MUTATED CORO7 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 5              84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D28V11, continuous
                 vv
clus               R0  R1  R2  RX
  CORO7 MUTATED     4   1   0   2
  CORO7 WILD-TYPE 133  12   2   5
D28V12, multiclass
    clus
vv   CORO7 MUTATED CORO7 WILD-TYPE
  R0             4             133
  R1             1              12
  R2             0               2
  RX             2               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CORO7 MUTATED       0                         0     6
  CORO7 WILD-TYPE    46                         5   108
D28V14, multiclass
                           clus
vv                          CORO7 MUTATED CORO7 WILD-TYPE
  ASIAN                                 0              46
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                 cls
clus               0  1
  CORO7 MUTATED    0  2
  CORO7 WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CORO7 MUTATED      0    2
  CORO7 WILD-TYPE    6   86
                        clus
vv                       CORO7 MUTATED CORO7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(29) Variable = ANAPC1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  ANAPC1 MUTATED     4   1
  ANAPC1 WILD-TYPE 104  76
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               5              180 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               1               76 
$`ANAPC1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3YC TCGA-JY-A6FD TCGA-L5-A4OJ TCGA-L5-A8NM 
       19.99        20.12        68.02        21.01         7.76 

$`ANAPC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
            7.76             0.13 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
           68.02           122.10 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
          20.120           12.885 
[1] "7.8 - 68.0 (20.1)"  "0.1 - 122.1 (12.9)"
[1] "hr=" "3.4"
D29V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANAPC1 MUTATED         1        0        0        0         1         1
  ANAPC1 WILD-TYPE       7        5        6        1        46        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC1 MUTATED           0          1          0          1        0
  ANAPC1 WILD-TYPE        26         13          9          6        5
                  vv
clus               STAGE IVA
  ANAPC1 MUTATED           0
  ANAPC1 WILD-TYPE         4
D29V3, multiclass
            clus
vv           ANAPC1 MUTATED ANAPC1 WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               1               46
  STAGE IIB               1               30
  STAGE III               0               26
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  ANAPC1 MUTATED       1  1  3  0
  ANAPC1 WILD-TYPE    31 42 85  5
D29V4, multiclass
       clus
vv      ANAPC1 MUTATED ANAPC1 WILD-TYPE
  T0+T1              1               31
  T2                 1               42
  T3                 3               85
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ANAPC1 MUTATED    2  2  0  1
  ANAPC1 WILD-TYPE 75 67 12  7
D29V5, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  N0              2               75
  N1              2               67
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     4   0
  ANAPC1 WILD-TYPE 132   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      4    0
  ANAPC1 WILD-TYPE  132    9
   clus
vv  ANAPC1 MUTATED ANAPC1 WILD-TYPE
  0              4              132
  1              0                9
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     3   2
  ANAPC1 WILD-TYPE  24 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      3    2
  ANAPC1 WILD-TYPE   24  156
        clus
vv       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  FEMALE              3               24
  MALE                2              156
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     5   0
  ANAPC1 WILD-TYPE 119  43
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      5    0
  ANAPC1 WILD-TYPE  119   43
     clus
vv    ANAPC1 MUTATED ANAPC1 WILD-TYPE
  NO               5              119
  YES              0               43
[1] 2 2
[1] FALSE
D29V9, continuous
[1] "Remove cluster labels:" "ANAPC1 MUTATED"        
clus
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
D29V10, binary
                  cls
clus                0  1
  ANAPC1 MUTATED    3  2
  ANAPC1 WILD-TYPE 86 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      3    2
  ANAPC1 WILD-TYPE   86   94
                                   clus
vv                                  ANAPC1 MUTATED ANAPC1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  3               86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              2               94
[1] 2 2
[1] FALSE
D29V11, continuous
[1] "Remove cluster labels:" "ANAPC1 MUTATED"        
clus
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A4P3       TCGA-IG-A4QT 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS       TCGA-IG-A8O2 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  ANAPC1 MUTATED     5   0   0   0
  ANAPC1 WILD-TYPE 132  13   2   7
D29V12, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  R0              5              132
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANAPC1 MUTATED       1                         0     4
  ANAPC1 WILD-TYPE    45                         5   110
D29V14, multiclass
                           clus
vv                          ANAPC1 MUTATED ANAPC1 WILD-TYPE
  ASIAN                                  1               45
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[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"
D29V15, binary
                  cls
clus                0  1
  ANAPC1 MUTATED    0  1
  ANAPC1 WILD-TYPE  6 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      0    1
  ANAPC1 WILD-TYPE    6   87
                        clus
vv                       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              1               87
[1] 2 2
[1] FALSE

Clustering(30) Variable = IVL MUTATION ANALYSIS
D30V1, survival
               sevent
clus2             0   1
  IVL MUTATED     5  10
  IVL WILD-TYPE 103  67
  IVL MUTATED IVL WILD-TYPE 
           15           170 
  IVL MUTATED IVL WILD-TYPE 
           10            67 
$`IVL MUTATED`
TCGA-L5-A4OI TCGA-S8-A6BV TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A93D 
       19.99        20.02         8.94        32.45         3.88        31.56 
TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NM 
       47.93         3.16         4.90         3.02        55.50         7.76 
TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-V5-AASX 
        9.30         5.29         8.98 

$`IVL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        7.63         5.92        13.94        16.24         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17         1.38        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  IVL MUTATED IVL WILD-TYPE 
         3.02          0.13 
  IVL MUTATED IVL WILD-TYPE 
         55.5         122.1 
  IVL MUTATED IVL WILD-TYPE 
         8.98         13.18 
[1] "3.0 - 55.5 (9.0)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "1.7"
D30V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IVL MUTATED         1        2        0        0         1         2
  IVL WILD-TYPE       7        3        6        1        46        29
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVL MUTATED           1          1          1          2        1         0
  IVL WILD-TYPE        25         13          8          5        4         4
D30V3, multiclass
            clus
vv           IVL MUTATED IVL WILD-TYPE
  STAGE I              1             7
  STAGE IA             2             3
  STAGE IB             0             6
  STAGE II             0             1
  STAGE IIA            1            46
  STAGE IIB            2            29
  STAGE III            1            25
  STAGE IIIA           1            13
  STAGE IIIB           1             8
  STAGE IIIC           2             5
  STAGE IV             1             4
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1 T2 T3 T4
  IVL MUTATED       4  3  6  0
  IVL WILD-TYPE    28 40 82  5
D30V4, multiclass
       clus
vv      IVL MUTATED IVL WILD-TYPE
  T0+T1           4            28
  T2              3            40
  T3              6            82
  T4              0             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  IVL MUTATED    4  6  1  2
  IVL WILD-TYPE 73 63 11  6
D30V5, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  N0           4            73
  N1           6            63
  N2           1            11
  N3           2             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
               cls
clus              0   1
  IVL MUTATED     7   1
  IVL WILD-TYPE 129   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED      7    1
  IVL WILD-TYPE  129    8
   clus
vv  IVL MUTATED IVL WILD-TYPE
  0           7           129
  1           1             8
[1] 2 2
[1] FALSE
D30V7, binary
               cls
clus              0   1
  IVL MUTATED     3  12
  IVL WILD-TYPE  24 146
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED      3   12
  IVL WILD-TYPE   24  146
        clus
vv       IVL MUTATED IVL WILD-TYPE
  FEMALE           3            24
  MALE            12           146
[1] 2 2
[1] FALSE
D30V8, binary
               cls
clus              0   1
  IVL MUTATED    13   1
  IVL WILD-TYPE 111  42
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     13    1
  IVL WILD-TYPE  111   42
     clus
vv    IVL MUTATED IVL WILD-TYPE
  NO           13           111
  YES           1            42
[1] 2 2
[1] FALSE
D30V9, continuous
[1] "Remove cluster labels:" "IVL MUTATED"           
clus
  IVL MUTATED IVL WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER    TCGA-VR-A8ET 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY    TCGA-VR-A8EZ 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" "IVL WILD-TYPE" 
   TCGA-Z6-A8JE 
"IVL WILD-TYPE" 
D30V10, binary
               cls
clus             0  1
  IVL MUTATED   14  1
  IVL WILD-TYPE 75 95
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     14    1
  IVL WILD-TYPE   75   95
                                   clus
vv                                  IVL MUTATED IVL WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS              14            75
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           1            95
[1] 2 2
[1] FALSE
D30V11, continuous
               vv
clus             R0  R1  R2  RX
  IVL MUTATED    11   2   0   0
  IVL WILD-TYPE 126  11   2   7
D30V12, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  R0          11           126
  R1           2            11
  R2           0             2
  RX           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IVL MUTATED       0                         0    12
  IVL WILD-TYPE    46                         5   102
D30V14, multiclass
                           clus
vv                          IVL MUTATED IVL WILD-TYPE
  ASIAN                               0            46
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                              12           102
[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"
D30V15, binary
               cls
clus             0  1
  IVL MUTATED    2  3
  IVL WILD-TYPE  4 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED      2    3
  IVL WILD-TYPE    4   85
                        clus
vv                       IVL MUTATED IVL WILD-TYPE
  HISPANIC OR LATINO               2             4
  NOT HISPANIC OR LATINO           3            85
[1] 2 2
[1] FALSE

Clustering(31) Variable = PIK3CA MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   10  9
  PIK3CA WILD-TYPE 98 68
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              166 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               68 
$`PIK3CA MUTATED`
TCGA-L5-A43J TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A7DP 
        4.31         7.69        35.21        20.78        18.64        14.86 
TCGA-JY-A6FG TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A8NH TCGA-L5-A8NW TCGA-LN-A49M 
       41.52         7.13        25.12        12.92        46.09        12.66 
TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-R6-A6KZ TCGA-V5-AASV TCGA-VR-A8EW TCGA-XP-A8T7 
       12.59        12.00         5.06        15.35         8.12        41.23 
TCGA-Z6-AAPN 
        2.66 

$`PIK3CA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        32.45        33.27         0.85         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.43        15.48         2.60         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        3.42         2.10         1.32        19.73 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.66             0.13 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           46.09           122.10 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          12.920           13.165 
[1] "2.7 - 46.1 (12.9)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CA MUTATED         0        0        1        0         6         5
  PIK3CA WILD-TYPE       8        5        5        1        41        26
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           2          2          1          0        1
  PIK3CA WILD-TYPE        24         12          8          7        4
                  vv
clus               STAGE IVA
  PIK3CA MUTATED           0
  PIK3CA WILD-TYPE         4
D31V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               6               41
  STAGE IIB               5               26
  STAGE III               2               24
  STAGE IIIA              2               12
  STAGE IIIB              1                8
  STAGE IIIC              0                7
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  PIK3CA MUTATED       2  7  7  2
  PIK3CA WILD-TYPE    30 36 81  3
D31V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1              2               30
  T2                 7               36
  T3                 7               81
  T4                 2                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   10  6  1  0
  PIK3CA WILD-TYPE 67 63 11  8
D31V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             10               67
  N1              6               63
  N2              1               11
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    13   1
  PIK3CA WILD-TYPE 123   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     13    1
  PIK3CA WILD-TYPE  123    8
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             13              123
  1              1                8
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     3  16
  PIK3CA WILD-TYPE  24 142
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3   16
  PIK3CA WILD-TYPE   24  142
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              3               24
  MALE               16              142
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    12   5
  PIK3CA WILD-TYPE 112  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     12    5
  PIK3CA WILD-TYPE  112   38
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              12              112
  YES              5               38
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, binary
                  cls
clus                0  1
  PIK3CA MUTATED    6 13
  PIK3CA WILD-TYPE 83 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      6   13
  PIK3CA WILD-TYPE   83   83
                                   clus
vv                                  PIK3CA MUTATED PIK3CA WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  6               83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             13               83
[1] 2 2
[1] FALSE
D31V11, continuous
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    15   1   0   1
  PIK3CA WILD-TYPE 122  12   2   6
D31V12, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             15              122
  R1              1               12
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       4                         1    13
  PIK3CA WILD-TYPE    42                         4   101
D31V14, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  4               42
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                 13              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                  cls
clus                0  1
  PIK3CA MUTATED    1 11
  PIK3CA WILD-TYPE  5 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   11
  PIK3CA WILD-TYPE    5   77
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11               77
[1] 2 2
[1] FALSE

Clustering(32) Variable = RB1 MUTATION ANALYSIS
D32V1, survival
               sevent
clus2             0   1
  RB1 MUTATED     7   0
  RB1 WILD-TYPE 101  77
  RB1 MUTATED RB1 WILD-TYPE 
            7           178 
  RB1 MUTATED RB1 WILD-TYPE 
            0            77 
$`RB1 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FD TCGA-L5-A893 TCGA-L5-A8NN TCGA-LN-A4MQ TCGA-VR-A8EP 
       19.99        68.02         3.02         5.49        12.33        27.09 
TCGA-Z6-A8JD 
        3.42 

$`RB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  RB1 MUTATED RB1 WILD-TYPE 
         3.02          0.13 
  RB1 MUTATED RB1 WILD-TYPE 
        68.02        122.10 
  RB1 MUTATED RB1 WILD-TYPE 
       12.330        13.165 
[1] "3.0 - 68.0 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr="     "2.6e+07"
D32V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RB1 MUTATED         1        0        0        0         1         1
  RB1 WILD-TYPE       7        5        6        1        46        30
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RB1 MUTATED           2          0          1          1        0         0
  RB1 WILD-TYPE        24         14          8          6        5         4
D32V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              1             7
  STAGE IA             0             5
  STAGE IB             0             6
  STAGE II             0             1
  STAGE IIA            1            46
  STAGE IIB            1            30
  STAGE III            2            24
  STAGE IIIA           0            14
  STAGE IIIB           1             8
  STAGE IIIC           1             6
  STAGE IV             0             5
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1 T2 T3 T4
  RB1 MUTATED       1  0  6  0
  RB1 WILD-TYPE    31 43 82  5
D32V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           1            31
  T2              0            43
  T3              6            82
  T4              0             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  RB1 MUTATED    3  2  1  1
  RB1 WILD-TYPE 74 67 11  7
D32V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           3            74
  N1           2            67
  N2           1            11
  N3           1             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
               cls
clus              0   1
  RB1 MUTATED     6   0
  RB1 WILD-TYPE 130   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      6    0
  RB1 WILD-TYPE  130    9
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0           6           130
  1           0             9
[1] 2 2
[1] FALSE
D32V7, binary
               cls
clus              0   1
  RB1 MUTATED     2   5
  RB1 WILD-TYPE  25 153
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      2    5
  RB1 WILD-TYPE   25  153
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           2            25
  MALE             5           153
[1] 2 2
[1] FALSE
D32V8, binary
               cls
clus              0   1
  RB1 MUTATED     7   0
  RB1 WILD-TYPE 117  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      7    0
  RB1 WILD-TYPE  117   43
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO            7           117
  YES           0            43
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, binary
               cls
clus             0  1
  RB1 MUTATED    3  4
  RB1 WILD-TYPE 86 92
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      3    4
  RB1 WILD-TYPE   86   92
                                   clus
vv                                  RB1 MUTATED RB1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS               3            86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           4            92
[1] 2 2
[1] FALSE
D32V11, continuous
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED     7   0   0   0
  RB1 WILD-TYPE 130  13   2   7
D32V12, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0           7           130
  R1           0            13
  R2           0             2
  RX           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       2                         0     5
  RB1 WILD-TYPE    44                         5   109
D32V14, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               2            44
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               5           109
[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"
D32V15, binary
               cls
clus             0  1
  RB1 MUTATED    0  2
  RB1 WILD-TYPE  6 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0    2
  RB1 WILD-TYPE    6   86
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           2            86
[1] 2 2
[1] FALSE

Clustering(33) Variable = EIF4EBP2 MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  EIF4EBP2 MUTATED     2   1
  EIF4EBP2 WILD-TYPE 106  76
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 3                182 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 1                 76 
$`EIF4EBP2 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OH TCGA-R6-A6L6 
       19.99        32.61         7.04 

$`EIF4EBP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
              7.04               0.13 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
             32.61             122.10 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
            19.990             13.035 
[1] "7.0 - 32.6 (20.0)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.5"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4EBP2 MUTATED         1        0        0        0         0         0
  EIF4EBP2 WILD-TYPE       7        5        6        1        47        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4EBP2 MUTATED           0          0          0          1        0
  EIF4EBP2 WILD-TYPE        26         14          9          6        5
                    vv
clus                 STAGE IVA
  EIF4EBP2 MUTATED           0
  EIF4EBP2 WILD-TYPE         4
D33V3, multiclass
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                161 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A4OE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A88T         TCGA-L5-A8NG 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-S8-A6BV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GF         TCGA-2H-A9GG         TCGA-2H-A9GH 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GI         TCGA-2H-A9GJ         TCGA-2H-A9GK 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GL         TCGA-2H-A9GM         TCGA-2H-A9GN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GO         TCGA-2H-A9GQ         TCGA-2H-A9GR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IC-A6RE         TCGA-IG-A3I8         TCGA-IG-A3QL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YB 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4QT         TCGA-IG-A50L         TCGA-IG-A51D 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A5S3         TCGA-IG-A625 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A6QS         TCGA-IG-A7DP         TCGA-IG-A8O2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-IG-A97I         TCGA-JY-A6F8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FD         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-JY-A939 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93C         TCGA-JY-A93D         TCGA-JY-A93E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93F         TCGA-KH-A6WC         TCGA-L5-A43E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OF         TCGA-L5-A4OJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OT         TCGA-L5-A4OU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A88W         TCGA-L5-A88Z 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NH         TCGA-L5-A8NI         TCGA-L5-A8NJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NL         TCGA-L5-A8NM 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NU         TCGA-L5-A8NV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-L7-A6VZ         TCGA-LN-A49K 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49L         TCGA-LN-A49M         TCGA-LN-A49N 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A49X         TCGA-LN-A49Y 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A1         TCGA-LN-A4A2         TCGA-LN-A4A3 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A4         TCGA-LN-A4A5         TCGA-LN-A4A6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A8         TCGA-LN-A4A9         TCGA-LN-A4MQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4MR         TCGA-LN-A5U5         TCGA-LN-A5U6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-LN-A8I1 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FO         TCGA-LN-A9FP         TCGA-LN-A9FQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FR         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-RE-A7BO         TCGA-S8-A6BW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-VR-A8EO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-A8JD         TCGA-Z6-A8JE         TCGA-Z6-A9VB 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-AAPN         TCGA-ZR-A9CJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
                    vv
clus                 T0+T1 T2 T3 T4
  EIF4EBP2 MUTATED       1  0  1  0
  EIF4EBP2 WILD-TYPE    31 43 87  5
D33V4, multiclass
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                166 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-S8-A6BV         TCGA-2H-A9GF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GG         TCGA-2H-A9GH         TCGA-2H-A9GI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GJ         TCGA-2H-A9GK         TCGA-2H-A9GL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GM         TCGA-2H-A9GN         TCGA-2H-A9GO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GQ         TCGA-2H-A9GR         TCGA-IC-A6RE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-IG-A4QT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A51D         TCGA-IG-A5B8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A625         TCGA-IG-A6QS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A7DP         TCGA-IG-A8O2         TCGA-IG-A97H 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A97I         TCGA-JY-A6F8         TCGA-JY-A6FA 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FD         TCGA-JY-A6FE         TCGA-JY-A6FG 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FH         TCGA-JY-A939         TCGA-JY-A93C 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93D         TCGA-JY-A93E         TCGA-JY-A93F 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43E         TCGA-L5-A43H 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OF         TCGA-L5-A4OJ         TCGA-L5-A4OM 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OR         TCGA-L5-A4OS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88W         TCGA-L5-A88Z         TCGA-L5-A891 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NH         TCGA-L5-A8NI         TCGA-L5-A8NJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NL         TCGA-L5-A8NM 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NU         TCGA-L5-A8NV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-L7-A6VZ         TCGA-LN-A49K 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49L         TCGA-LN-A49M         TCGA-LN-A49N 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A49X         TCGA-LN-A49Y 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A1         TCGA-LN-A4A2         TCGA-LN-A4A3 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A4         TCGA-LN-A4A5         TCGA-LN-A4A6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A8         TCGA-LN-A4A9         TCGA-LN-A4MQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4MR         TCGA-LN-A5U5         TCGA-LN-A5U6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-LN-A8I1 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FO         TCGA-LN-A9FP         TCGA-LN-A9FQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FR         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-RE-A7BO         TCGA-S8-A6BW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RE         TCGA-V5-AASV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-A8JE         TCGA-Z6-A9VB         TCGA-Z6-AAPN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-ZR-A9CJ 
"EIF4EBP2 WILD-TYPE" 
                    vv
clus                 N0 N1 N2 N3
  EIF4EBP2 MUTATED    1  0  0  1
  EIF4EBP2 WILD-TYPE 76 69 12  7
D33V5, multiclass
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                164 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-S8-A6BV         TCGA-2H-A9GF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GG         TCGA-2H-A9GH         TCGA-2H-A9GI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GJ         TCGA-2H-A9GK         TCGA-2H-A9GL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GM         TCGA-2H-A9GN         TCGA-2H-A9GO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GQ         TCGA-2H-A9GR         TCGA-IC-A6RE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-IG-A4QT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A51D         TCGA-IG-A5B8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A625         TCGA-IG-A6QS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97I         TCGA-JY-A6F8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FD         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-JY-A939 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93C         TCGA-JY-A93D         TCGA-JY-A93E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93F         TCGA-KH-A6WC         TCGA-L5-A43E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OF         TCGA-L5-A4OJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OT         TCGA-L5-A4OU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A88W         TCGA-L5-A88Z 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A891         TCGA-L5-A893         TCGA-L5-A8NE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NH         TCGA-L5-A8NI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NJ         TCGA-L5-A8NK         TCGA-L5-A8NL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NM         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NV         TCGA-L5-A8NW         TCGA-L7-A6VZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8I1         TCGA-LN-A9FO         TCGA-LN-A9FP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FQ         TCGA-LN-A9FR         TCGA-M9-A5M8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A8W5         TCGA-RE-A7BO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-S8-A6BW         TCGA-V5-A7RB         TCGA-V5-A7RE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EO         TCGA-VR-A8EP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-A8JD         TCGA-Z6-A8JE         TCGA-Z6-A9VB 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-AAPN         TCGA-ZR-A9CJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
D33V6, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     1   0
  EIF4EBP2 WILD-TYPE 135   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      1    0
  EIF4EBP2 WILD-TYPE  135    9
   clus
vv  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  0                1                135
  1                0                  9
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     0   3
  EIF4EBP2 WILD-TYPE  27 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      0    3
  EIF4EBP2 WILD-TYPE   27  155
        clus
vv       EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  FEMALE                0                 27
  MALE                  3                155
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     3   0
  EIF4EBP2 WILD-TYPE 121  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      3    0
  EIF4EBP2 WILD-TYPE  121   43
     clus
vv    EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  NO                 3                121
  YES                0                 43
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, binary
                    cls
clus                  0  1
  EIF4EBP2 MUTATED    3  0
  EIF4EBP2 WILD-TYPE 86 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      3    0
  EIF4EBP2 WILD-TYPE   86   96
                                   clus
vv                                  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    3                 86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                0                 96
[1] 2 2
[1] FALSE
D33V11, continuous
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  EIF4EBP2 MUTATED     2   0   0   0
  EIF4EBP2 WILD-TYPE 135  13   2   7
D33V12, multiclass
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                157 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-S8-A6BV         TCGA-2H-A9GF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GG         TCGA-2H-A9GH         TCGA-2H-A9GI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GJ         TCGA-2H-A9GK         TCGA-2H-A9GL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GM         TCGA-2H-A9GN         TCGA-2H-A9GO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GQ         TCGA-2H-A9GR         TCGA-IC-A6RE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-IG-A4QT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A51D         TCGA-IG-A5B8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A625         TCGA-IG-A6QS         TCGA-IG-A8O2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-IG-A97I         TCGA-JY-A6F8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FD         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-JY-A939 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93C         TCGA-JY-A93D         TCGA-JY-A93E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93F         TCGA-L5-A43C         TCGA-L5-A43E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OJ         TCGA-L5-A4OM 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OR         TCGA-L5-A4OS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88W         TCGA-L5-A88Z         TCGA-L5-A891 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NH         TCGA-L5-A8NI         TCGA-L5-A8NJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NL         TCGA-L5-A8NM 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NU         TCGA-L5-A8NV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-L7-A6VZ         TCGA-LN-A49K 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49L         TCGA-LN-A49M         TCGA-LN-A49N 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8I1         TCGA-LN-A9FO         TCGA-LN-A9FP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FQ         TCGA-LN-A9FR         TCGA-M9-A5M8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-RE-A7BO         TCGA-S8-A6BW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RE         TCGA-V5-AASV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7B 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-A8JE         TCGA-Z6-A9VB         TCGA-Z6-AAPN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-ZR-A9CJ 
"EIF4EBP2 WILD-TYPE" 
D33V13, continuous
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                133 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-S8-A6BV         TCGA-2H-A9GF 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GG         TCGA-2H-A9GH         TCGA-2H-A9GI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GJ         TCGA-2H-A9GK         TCGA-2H-A9GL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GM         TCGA-2H-A9GN         TCGA-2H-A9GO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-2H-A9GQ         TCGA-2H-A9GR         TCGA-IC-A6RE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QS         TCGA-IG-A4QT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A51D         TCGA-IG-A5B8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A625         TCGA-IG-A6QS 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97I         TCGA-JY-A6F8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FD         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-JY-A939 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93C         TCGA-JY-A93D         TCGA-JY-A93E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A93F         TCGA-L5-A43C         TCGA-L5-A43E 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OF         TCGA-L5-A4OJ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OS         TCGA-L5-A4OT         TCGA-L5-A4OU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A88W         TCGA-L5-A88Z 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A891         TCGA-L5-A893         TCGA-L5-A8NE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NH         TCGA-L5-A8NI 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NJ         TCGA-L5-A8NK         TCGA-L5-A8NL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NM         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-L7-A6VZ         TCGA-LN-A49N 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49W         TCGA-LN-A4A3 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A4         TCGA-LN-A4MQ         TCGA-LN-A5U5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A7HY         TCGA-LN-A8I0 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A9FR         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-S8-A6BW         TCGA-V5-A7RB 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-VR-A8EO         TCGA-VR-A8EP 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Z6-A8JD         TCGA-Z6-A8JE         TCGA-Z6-AAPN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-ZR-A9CJ 
"EIF4EBP2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF4EBP2 MUTATED       0                         0     3
  EIF4EBP2 WILD-TYPE    46                         5   111
D33V14, multiclass
                           clus
vv                          EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  ASIAN                                    0                 46
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[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"
D33V15, binary
                    cls
clus                  0  1
  EIF4EBP2 MUTATED    0  1
  EIF4EBP2 WILD-TYPE  6 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      0    1
  EIF4EBP2 WILD-TYPE    6   87
                        clus
vv                       EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  HISPANIC OR LATINO                    0                  6
  NOT HISPANIC OR LATINO                1                 87
[1] 2 2
[1] FALSE

Clustering(34) Variable = SCD MUTATION ANALYSIS
D34V1, survival
               sevent
clus2             0   1
  SCD MUTATED     2   1
  SCD WILD-TYPE 106  76
  SCD MUTATED SCD WILD-TYPE 
            3           182 
  SCD MUTATED SCD WILD-TYPE 
            1            76 
$`SCD MUTATED`
TCGA-L5-A4OI TCGA-IG-A625 TCGA-L5-A8NR 
       19.99        12.82         8.71 

$`SCD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  SCD MUTATED SCD WILD-TYPE 
         8.71          0.13 
  SCD MUTATED SCD WILD-TYPE 
        19.99        122.10 
  SCD MUTATED SCD WILD-TYPE 
       12.820        13.165 
[1] "8.7 - 20.0 (12.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D34V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCD MUTATED         0        0        0        0         0         0
  SCD WILD-TYPE       8        5        6        1        47        31
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCD MUTATED           1          0          1          1        0         0
  SCD WILD-TYPE        25         14          8          6        5         4
D34V3, multiclass
            clus
vv           SCD MUTATED SCD WILD-TYPE
  STAGE I              0             8
  STAGE IA             0             5
  STAGE IB             0             6
  STAGE II             0             1
  STAGE IIA            0            47
  STAGE IIB            0            31
  STAGE III            1            25
  STAGE IIIA           0            14
  STAGE IIIB           1             8
  STAGE IIIC           1             6
  STAGE IV             0             5
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1 T2 T3 T4
  SCD MUTATED       0  0  3  0
  SCD WILD-TYPE    32 43 85  5
D34V4, multiclass
       clus
vv      SCD MUTATED SCD WILD-TYPE
  T0+T1           0            32
  T2              0            43
  T3              3            85
  T4              0             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  SCD MUTATED    0  1  1  1
  SCD WILD-TYPE 77 68 11  7
D34V5, multiclass
    clus
vv   SCD MUTATED SCD WILD-TYPE
  N0           0            77
  N1           1            68
  N2           1            11
  N3           1             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
               cls
clus              0   1
  SCD MUTATED     2   0
  SCD WILD-TYPE 134   9
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      2    0
  SCD WILD-TYPE  134    9
   clus
vv  SCD MUTATED SCD WILD-TYPE
  0           2           134
  1           0             9
[1] 2 2
[1] FALSE
D34V7, binary
               cls
clus              0   1
  SCD MUTATED     1   2
  SCD WILD-TYPE  26 156
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      1    2
  SCD WILD-TYPE   26  156
        clus
vv       SCD MUTATED SCD WILD-TYPE
  FEMALE           1            26
  MALE             2           156
[1] 2 2
[1] FALSE
D34V8, binary
               cls
clus              0   1
  SCD MUTATED     2   0
  SCD WILD-TYPE 122  43
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      2    0
  SCD WILD-TYPE  122   43
     clus
vv    SCD MUTATED SCD WILD-TYPE
  NO            2           122
  YES           0            43
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, binary
               cls
clus             0  1
  SCD MUTATED    2  1
  SCD WILD-TYPE 87 95
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      2    1
  SCD WILD-TYPE   87   95
                                   clus
vv                                  SCD MUTATED SCD WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS               2            87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA           1            95
[1] 2 2
[1] FALSE
D34V11, continuous
[1] "Remove cluster labels:" "SCD MUTATED"           
clus
  SCD MUTATED SCD WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NS    TCGA-L5-A8NW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6    TCGA-LN-A4A9 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8    TCGA-Q9-A6FW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-Z6-AAPN 
"SCD WILD-TYPE" 
               vv
clus             R0  R1  R2  RX
  SCD MUTATED     3   0   0   0
  SCD WILD-TYPE 134  13   2   7
D34V12, multiclass
    clus
vv   SCD MUTATED SCD WILD-TYPE
  R0           3           134
  R1           0            13
  R2           0             2
  RX           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCD MUTATED       1                         0     1
  SCD WILD-TYPE    45                         5   113
D34V14, multiclass
[1] "Remove cluster labels:" "SCD MUTATED"           
clus
  SCD MUTATED SCD WILD-TYPE 
            2           163 
   TCGA-IC-A6RF    TCGA-JY-A6FB    TCGA-JY-A938    TCGA-L5-A43I    TCGA-L5-A43J 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A4OE    TCGA-L5-A4OG    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A8NT    TCGA-Q9-A6FU    TCGA-S8-A6BV    TCGA-IC-A6RE    TCGA-IG-A3I8 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB    TCGA-IG-A3YC 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QS    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A51D 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A5B8    TCGA-IG-A5S3    TCGA-IG-A6QS    TCGA-IG-A7DP    TCGA-IG-A8O2 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IG-A97H    TCGA-IG-A97I    TCGA-JY-A6F8    TCGA-JY-A6FA    TCGA-JY-A6FD 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-JY-A6FE    TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-JY-A939    TCGA-JY-A93C 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-JY-A93D    TCGA-JY-A93E    TCGA-JY-A93F    TCGA-KH-A6WC    TCGA-L5-A43C 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A43E    TCGA-L5-A43H    TCGA-L5-A4OF    TCGA-L5-A4OH    TCGA-L5-A4OJ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP    TCGA-L5-A4OQ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A4OR    TCGA-L5-A4OS    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OX 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A88W    TCGA-L5-A88Z    TCGA-L5-A891 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF    TCGA-L5-A8NH    TCGA-L5-A8NI 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A8NJ    TCGA-L5-A8NK    TCGA-L5-A8NL    TCGA-L5-A8NM    TCGA-L5-A8NN 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L5-A8NQ    TCGA-L5-A8NS    TCGA-L5-A8NU    TCGA-L5-A8NV    TCGA-L5-A8NW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-L7-A56G    TCGA-L7-A6VZ    TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A49N    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-LN-A8I1    TCGA-LN-A9FO    TCGA-LN-A9FP    TCGA-LN-A9FQ    TCGA-LN-A9FR 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6DQ    TCGA-R6-A6KZ    TCGA-R6-A6L4 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-R6-A6L6    TCGA-R6-A6XG    TCGA-R6-A6XQ    TCGA-R6-A6Y0    TCGA-R6-A6Y2 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-R6-A8WG    TCGA-RE-A7BO 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-S8-A6BW    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ET 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EY    TCGA-VR-A8EZ    TCGA-VR-A8Q7 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7I    TCGA-X8-AAAR 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-Z6-A9VB    TCGA-Z6-AAPN    TCGA-ZR-A9CJ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
D34V15, binary
               cls
clus             0  1
  SCD MUTATED    0  1
  SCD WILD-TYPE  6 87
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      0    1
  SCD WILD-TYPE    6   87
                        clus
vv                       SCD MUTATED SCD WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           1            87
[1] 2 2
[1] FALSE

Clustering(35) Variable = MKL2 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  MKL2 MUTATED     3   3
  MKL2 WILD-TYPE 105  74
  MKL2 MUTATED MKL2 WILD-TYPE 
             6            179 
  MKL2 MUTATED MKL2 WILD-TYPE 
             3             74 
$`MKL2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NG TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-R6-A6L6 
        4.31        19.99        35.97       122.10         7.76         7.04 

$`MKL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82         0.36        27.12         5.16        20.02 
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  MKL2 MUTATED MKL2 WILD-TYPE 
          4.31           0.13 
  MKL2 MUTATED MKL2 WILD-TYPE 
        122.10          83.24 
  MKL2 MUTATED MKL2 WILD-TYPE 
        13.875         13.150 
[1] "4.3 - 122.1 (13.9)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.3"
D35V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MKL2 MUTATED         1        0        0        0         0         2
  MKL2 WILD-TYPE       7        5        6        1        47        29
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKL2 MUTATED           1          0          0          1        0         0
  MKL2 WILD-TYPE        25         14          9          6        5         4
D35V3, multiclass
            clus
vv           MKL2 MUTATED MKL2 WILD-TYPE
  STAGE I               1              7
  STAGE IA              0              5
  STAGE IB              0              6
  STAGE II              0              1
  STAGE IIA             0             47
  STAGE IIB             2             29
  STAGE III             1             25
  STAGE IIIA            0             14
  STAGE IIIB            0              9
  STAGE IIIC            1              6
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  MKL2 MUTATED       1  1  3  0
  MKL2 WILD-TYPE    31 42 85  5
D35V4, multiclass
       clus
vv      MKL2 MUTATED MKL2 WILD-TYPE
  T0+T1            1             31
  T2               1             42
  T3               3             85
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MKL2 MUTATED    2  2  0  1
  MKL2 WILD-TYPE 75 67 12  7
D35V5, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  N0            2             75
  N1            2             67
  N2            0             12
  N3            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                cls
clus               0   1
  MKL2 MUTATED     3   0
  MKL2 WILD-TYPE 133   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      3    0
  MKL2 WILD-TYPE  133    9
   clus
vv  MKL2 MUTATED MKL2 WILD-TYPE
  0            3            133
  1            0              9
[1] 2 2
[1] FALSE
D35V7, binary
                cls
clus               0   1
  MKL2 MUTATED     1   5
  MKL2 WILD-TYPE  26 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      1    5
  MKL2 WILD-TYPE   26  153
        clus
vv       MKL2 MUTATED MKL2 WILD-TYPE
  FEMALE            1             26
  MALE              5            153
[1] 2 2
[1] FALSE
D35V8, binary
                cls
clus               0   1
  MKL2 MUTATED     5   0
  MKL2 WILD-TYPE 119  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      5    0
  MKL2 WILD-TYPE  119   43
     clus
vv    MKL2 MUTATED MKL2 WILD-TYPE
  NO             5            119
  YES            0             43
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, binary
                cls
clus              0  1
  MKL2 MUTATED    5  1
  MKL2 WILD-TYPE 84 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      5    1
  MKL2 WILD-TYPE   84   95
                                   clus
vv                                  MKL2 MUTATED MKL2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                5             84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            1             95
[1] 2 2
[1] FALSE
D35V11, continuous
                vv
clus              R0  R1  R2  RX
  MKL2 MUTATED     4   0   0   1
  MKL2 WILD-TYPE 133  13   2   6
D35V12, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  R0            4            133
  R1            0             13
  R2            0              2
  RX            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MKL2 MUTATED       0                         0     6
  MKL2 WILD-TYPE    46                         5   108
D35V14, multiclass
                           clus
vv                          MKL2 MUTATED MKL2 WILD-TYPE
  ASIAN                                0             46
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                cls
clus              0  1
  MKL2 MUTATED    0  1
  MKL2 WILD-TYPE  6 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      0    1
  MKL2 WILD-TYPE    6   87
                        clus
vv                       MKL2 MUTATED MKL2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            1             87
[1] 2 2
[1] FALSE

Clustering(36) Variable = NOTCH1 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  NOTCH1 MUTATED   12  6
  NOTCH1 WILD-TYPE 96 71
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              18              167 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               6               71 
$`NOTCH1 MUTATED`
TCGA-L5-A43J TCGA-L5-A88T TCGA-2H-A9GN TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5S3 
        4.31        22.82         8.94         0.85         0.53        23.41 
TCGA-KH-A6WC TCGA-L5-A4OU TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A1 
        6.28        29.00        10.85        12.43        12.59        12.59 
TCGA-LN-A5U6 TCGA-LN-A9FR TCGA-R6-A6Y2 TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.33        12.26         9.30        15.35        33.70        18.18 

$`NOTCH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
       18.64         3.88         9.30        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        10.45        12.66        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.53             0.13 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            33.7            122.1 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
           12.38            13.22 
[1] "0.5 - 33.7 (12.4)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1"  
D36V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOTCH1 MUTATED         0        1        0        0         4         7
  NOTCH1 WILD-TYPE       8        4        6        1        43        24
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOTCH1 MUTATED           1          2          0          1        0
  NOTCH1 WILD-TYPE        25         12          9          6        5
                  vv
clus               STAGE IVA
  NOTCH1 MUTATED           0
  NOTCH1 WILD-TYPE         4
D36V3, multiclass
            clus
vv           NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                1                4
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               4               43
  STAGE IIB               7               24
  STAGE III               1               25
  STAGE IIIA              2               12
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  NOTCH1 MUTATED       1  4 10  1
  NOTCH1 WILD-TYPE    31 39 78  4
D36V4, multiclass
       clus
vv      NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T0+T1              1               31
  T2                 4               39
  T3                10               78
  T4                 1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NOTCH1 MUTATED    9  6  0  1
  NOTCH1 WILD-TYPE 68 63 12  7
D36V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0              9               68
  N1              6               63
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    14   0
  NOTCH1 WILD-TYPE 122   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     14    0
  NOTCH1 WILD-TYPE  122    9
   clus
vv  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  0             14              122
  1              0                9
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     2  16
  NOTCH1 WILD-TYPE  25 142
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      2   16
  NOTCH1 WILD-TYPE   25  142
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE              2               25
  MALE               16              142
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    10   6
  NOTCH1 WILD-TYPE 114  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     10    6
  NOTCH1 WILD-TYPE  114   37
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              10              114
  YES              6               37
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, binary
                  cls
clus                0  1
  NOTCH1 MUTATED    4 14
  NOTCH1 WILD-TYPE 85 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      4   14
  NOTCH1 WILD-TYPE   85   82
                                   clus
vv                                  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  4               85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             14               82
[1] 2 2
[1] FALSE
D36V11, continuous
                  vv
clus                R0  R1  R2  RX
  NOTCH1 MUTATED    11   0   0   1
  NOTCH1 WILD-TYPE 126  13   2   6
D36V12, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  R0             11              126
  R1              0               13
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED       6                         2     9
  NOTCH1 WILD-TYPE    40                         3   105
D36V14, multiclass
                           clus
vv                          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASIAN                                  6               40
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                  cls
clus                0  1
  NOTCH1 MUTATED    1 11
  NOTCH1 WILD-TYPE  5 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      1   11
  NOTCH1 WILD-TYPE    5   77
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11               77
[1] 2 2
[1] FALSE

Clustering(37) Variable = KLF3 MUTATION ANALYSIS
D37V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED     2   1
  KLF3 WILD-TYPE 106  76
  KLF3 MUTATED KLF3 WILD-TYPE 
             3            182 
  KLF3 MUTATED KLF3 WILD-TYPE 
             1             76 
$`KLF3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NG TCGA-L5-A8NM 
       19.99        35.97         7.76 

$`KLF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  KLF3 MUTATED KLF3 WILD-TYPE 
          7.76           0.13 
  KLF3 MUTATED KLF3 WILD-TYPE 
         35.97         122.10 
  KLF3 MUTATED KLF3 WILD-TYPE 
        19.990         13.035 
[1] "7.8 - 36.0 (20.0)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.6"
D37V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLF3 MUTATED         0        0        0        0         0         1
  KLF3 WILD-TYPE       8        5        6        1        47        30
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF3 MUTATED           1          0          0          1        0         0
  KLF3 WILD-TYPE        25         14          9          6        5         4
D37V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0              8
  STAGE IA              0              5
  STAGE IB              0              6
  STAGE II              0              1
  STAGE IIA             0             47
  STAGE IIB             1             30
  STAGE III             1             25
  STAGE IIIA            0             14
  STAGE IIIB            0              9
  STAGE IIIC            1              6
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  KLF3 MUTATED       0  1  2  0
  KLF3 WILD-TYPE    32 42 86  5
D37V4, multiclass
       clus
vv      KLF3 MUTATED KLF3 WILD-TYPE
  T0+T1            0             32
  T2               1             42
  T3               2             86
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KLF3 MUTATED    0  2  0  1
  KLF3 WILD-TYPE 77 67 12  7
D37V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0            0             77
  N1            2             67
  N2            0             12
  N3            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                cls
clus               0   1
  KLF3 MUTATED     2   0
  KLF3 WILD-TYPE 134   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      2    0
  KLF3 WILD-TYPE  134    9
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0            2            134
  1            0              9
[1] 2 2
[1] FALSE
D37V7, binary
                cls
clus               0   1
  KLF3 MUTATED     1   2
  KLF3 WILD-TYPE  26 156
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      1    2
  KLF3 WILD-TYPE   26  156
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE            1             26
  MALE              2            156
[1] 2 2
[1] FALSE
D37V8, binary
                cls
clus               0   1
  KLF3 MUTATED     3   0
  KLF3 WILD-TYPE 121  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      3    0
  KLF3 WILD-TYPE  121   43
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO             3            121
  YES            0             43
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, binary
                cls
clus              0  1
  KLF3 MUTATED    3  0
  KLF3 WILD-TYPE 86 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      3    0
  KLF3 WILD-TYPE   86   96
                                   clus
vv                                  KLF3 MUTATED KLF3 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                3             86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            0             96
[1] 2 2
[1] FALSE
D37V11, continuous
[1] "Remove cluster labels:" "KLF3 MUTATED"          
clus
  KLF3 MUTATED KLF3 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL     TCGA-IG-A3Y9 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED     3   0   0   0
  KLF3 WILD-TYPE 134  13   2   7
D37V12, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0            3            134
  R1            0             13
  R2            0              2
  RX            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF3 MUTATED       0                         0     3
  KLF3 WILD-TYPE    46                         5   111
D37V14, multiclass
                           clus
vv                          KLF3 MUTATED KLF3 WILD-TYPE
  ASIAN                                0             46
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[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"
D37V15, binary
                cls
clus              0  1
  KLF3 MUTATED    0  0
  KLF3 WILD-TYPE  6 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      0    0
  KLF3 WILD-TYPE    6   88

Clustering(38) Variable = IL10RA MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  IL10RA MUTATED     1   2
  IL10RA WILD-TYPE 107  75
  IL10RA MUTATED IL10RA WILD-TYPE 
               3              182 
  IL10RA MUTATED IL10RA WILD-TYPE 
               2               75 
$`IL10RA MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OH TCGA-VR-A8EQ 
       18.64        32.61        22.82 

$`IL10RA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  IL10RA MUTATED IL10RA WILD-TYPE 
           18.64             0.13 
  IL10RA MUTATED IL10RA WILD-TYPE 
           32.61           122.10 
  IL10RA MUTATED IL10RA WILD-TYPE 
          22.820           12.885 
[1] "18.6 - 32.6 (22.8)" "0.1 - 122.1 (12.9)"
[1] "hr=" "1"  
D38V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL10RA MUTATED         1        0        0        0         0         1
  IL10RA WILD-TYPE       7        5        6        1        47        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL10RA MUTATED           1          0          0          0        0
  IL10RA WILD-TYPE        25         14          9          7        5
                  vv
clus               STAGE IVA
  IL10RA MUTATED           0
  IL10RA WILD-TYPE         4
D38V3, multiclass
            clus
vv           IL10RA MUTATED IL10RA WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               0               47
  STAGE IIB               1               30
  STAGE III               1               25
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              0                7
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  IL10RA MUTATED       1  1  1  0
  IL10RA WILD-TYPE    31 42 87  5
D38V4, multiclass
       clus
vv      IL10RA MUTATED IL10RA WILD-TYPE
  T0+T1              1               31
  T2                 1               42
  T3                 1               87
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  IL10RA MUTATED    1  2  0  0
  IL10RA WILD-TYPE 76 67 12  8
D38V5, multiclass
    clus
vv   IL10RA MUTATED IL10RA WILD-TYPE
  N0              1               76
  N1              2               67
  N2              0               12
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                  cls
clus                 0   1
  IL10RA MUTATED     3   0
  IL10RA WILD-TYPE 133   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RA MUTATED      3    0
  IL10RA WILD-TYPE  133    9
   clus
vv  IL10RA MUTATED IL10RA WILD-TYPE
  0              3              133
  1              0                9
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                 0   1
  IL10RA MUTATED     0   3
  IL10RA WILD-TYPE  27 155
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RA MUTATED      0    3
  IL10RA WILD-TYPE   27  155
        clus
vv       IL10RA MUTATED IL10RA WILD-TYPE
  FEMALE              0               27
  MALE                3              155
[1] 2 2
[1] FALSE
D38V8, binary
                  cls
clus                 0   1
  IL10RA MUTATED     1   2
  IL10RA WILD-TYPE 123  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RA MUTATED      1    2
  IL10RA WILD-TYPE  123   41
     clus
vv    IL10RA MUTATED IL10RA WILD-TYPE
  NO               1              123
  YES              2               41
[1] 2 2
[1] FALSE
D38V9, continuous
[1] "Remove cluster labels:" "IL10RA MUTATED"        
clus
  IL10RA MUTATED IL10RA WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
D38V10, binary
                  cls
clus                0  1
  IL10RA MUTATED    2  1
  IL10RA WILD-TYPE 87 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RA MUTATED      2    1
  IL10RA WILD-TYPE   87   95
                                   clus
vv                                  IL10RA MUTATED IL10RA WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  2               87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              1               95
[1] 2 2
[1] FALSE
D38V11, continuous
[1] "Remove cluster labels:" "IL10RA MUTATED"        
clus
  IL10RA MUTATED IL10RA WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OM       TCGA-L5-A4ON 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" "IL10RA WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  IL10RA MUTATED     3   0   0   0
  IL10RA WILD-TYPE 134  13   2   7
D38V12, multiclass
    clus
vv   IL10RA MUTATED IL10RA WILD-TYPE
  R0              3              134
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL10RA MUTATED       0                         0     3
  IL10RA WILD-TYPE    46                         5   111
D38V14, multiclass
                           clus
vv                          IL10RA MUTATED IL10RA WILD-TYPE
  ASIAN                                  0               46
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[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"
D38V15, binary
                  cls
clus                0  1
  IL10RA MUTATED    0  1
  IL10RA WILD-TYPE  6 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL10RA MUTATED      0    1
  IL10RA WILD-TYPE    6   87
                        clus
vv                       IL10RA MUTATED IL10RA WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              1               87
[1] 2 2
[1] FALSE

Clustering(39) Variable = RAD17 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  RAD17 MUTATED     4   0
  RAD17 WILD-TYPE 104  77
  RAD17 MUTATED RAD17 WILD-TYPE 
              4             181 
  RAD17 MUTATED RAD17 WILD-TYPE 
              0              77 
$`RAD17 MUTATED`
TCGA-IC-A6RE TCGA-LN-A7HX TCGA-VR-A8Q7 TCGA-Z6-A8JE 
        7.69        12.23        52.27         2.10 

$`RAD17 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  RAD17 MUTATED RAD17 WILD-TYPE 
           2.10            0.13 
  RAD17 MUTATED RAD17 WILD-TYPE 
          52.27          122.10 
  RAD17 MUTATED RAD17 WILD-TYPE 
           9.96           13.18 
[1] "2.1 - 52.3 (10.0)"  "0.1 - 122.1 (13.2)"
[1] "hr="     "9400000"
D39V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAD17 MUTATED         0        0        0        0         1         1
  RAD17 WILD-TYPE       8        5        6        1        46        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAD17 MUTATED           0          2          0          0        0         0
  RAD17 WILD-TYPE        26         12          9          7        5         4
D39V3, multiclass
            clus
vv           RAD17 MUTATED RAD17 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              1              30
  STAGE III              0              26
  STAGE IIIA             2              12
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  RAD17 MUTATED       1  1  2  0
  RAD17 WILD-TYPE    31 42 86  5
D39V4, multiclass
       clus
vv      RAD17 MUTATED RAD17 WILD-TYPE
  T0+T1             1              31
  T2                1              42
  T3                2              86
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RAD17 MUTATED    1  3  0  0
  RAD17 WILD-TYPE 76 66 12  8
D39V5, multiclass
    clus
vv   RAD17 MUTATED RAD17 WILD-TYPE
  N0             1              76
  N1             3              66
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                 cls
clus                0   1
  RAD17 MUTATED     4   0
  RAD17 WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      4    0
  RAD17 WILD-TYPE  132    9
   clus
vv  RAD17 MUTATED RAD17 WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus                0   1
  RAD17 MUTATED     0   4
  RAD17 WILD-TYPE  27 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      0    4
  RAD17 WILD-TYPE   27  154
        clus
vv       RAD17 MUTATED RAD17 WILD-TYPE
  FEMALE             0              27
  MALE               4             154
[1] 2 2
[1] FALSE
D39V8, binary
                 cls
clus                0   1
  RAD17 MUTATED     3   1
  RAD17 WILD-TYPE 121  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      3    1
  RAD17 WILD-TYPE  121   42
     clus
vv    RAD17 MUTATED RAD17 WILD-TYPE
  NO              3             121
  YES             1              42
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, binary
                 cls
clus               0  1
  RAD17 MUTATED    1  3
  RAD17 WILD-TYPE 88 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      1    3
  RAD17 WILD-TYPE   88   93
                                   clus
vv                                  RAD17 MUTATED RAD17 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 1              88
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             3              93
[1] 2 2
[1] FALSE
D39V11, continuous
                 vv
clus               R0  R1  R2  RX
  RAD17 MUTATED     3   0   0   1
  RAD17 WILD-TYPE 134  13   2   6
D39V12, multiclass
    clus
vv   RAD17 MUTATED RAD17 WILD-TYPE
  R0             3             134
  R1             0              13
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD17 MUTATED       1                         0     3
  RAD17 WILD-TYPE    45                         5   111
D39V14, multiclass
                           clus
vv                          RAD17 MUTATED RAD17 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[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"
D39V15, binary
                 cls
clus               0  1
  RAD17 MUTATED    0  3
  RAD17 WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      0    3
  RAD17 WILD-TYPE    6   85
                        clus
vv                       RAD17 MUTATED RAD17 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(40) Variable = KPNB1 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  KPNB1 MUTATED     3   3
  KPNB1 WILD-TYPE 105  74
  KPNB1 MUTATED KPNB1 WILD-TYPE 
              6             179 
  KPNB1 MUTATED KPNB1 WILD-TYPE 
              3              74 
$`KPNB1 MUTATED`
TCGA-IG-A4P3 TCGA-JY-A93C TCGA-L5-A43H TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A5U7 
       18.64        23.18         0.30         5.92        12.59        25.25 

$`KPNB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  KPNB1 MUTATED KPNB1 WILD-TYPE 
           0.30            0.13 
  KPNB1 MUTATED KPNB1 WILD-TYPE 
          25.25          122.10 
  KPNB1 MUTATED KPNB1 WILD-TYPE 
         15.615          13.150 
[1] "0.3 - 25.2 (15.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.4"
D40V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KPNB1 MUTATED         0        0        0        0         3         1
  KPNB1 WILD-TYPE       8        5        6        1        44        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNB1 MUTATED           1          0          1          0        0         0
  KPNB1 WILD-TYPE        25         14          8          7        5         4
D40V3, multiclass
            clus
vv           KPNB1 MUTATED KPNB1 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              3              44
  STAGE IIB              1              30
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             1               8
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  KPNB1 MUTATED       0  2  4  0
  KPNB1 WILD-TYPE    32 41 84  5
D40V4, multiclass
       clus
vv      KPNB1 MUTATED KPNB1 WILD-TYPE
  T0+T1             0              32
  T2                2              41
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KPNB1 MUTATED    3  2  1  0
  KPNB1 WILD-TYPE 74 67 11  8
D40V5, multiclass
    clus
vv   KPNB1 MUTATED KPNB1 WILD-TYPE
  N0             3              74
  N1             2              67
  N2             1              11
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                 cls
clus                0   1
  KPNB1 MUTATED     6   0
  KPNB1 WILD-TYPE 130   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNB1 MUTATED      6    0
  KPNB1 WILD-TYPE  130    9
   clus
vv  KPNB1 MUTATED KPNB1 WILD-TYPE
  0             6             130
  1             0               9
[1] 2 2
[1] FALSE
D40V7, binary
                 cls
clus                0   1
  KPNB1 MUTATED     0   6
  KPNB1 WILD-TYPE  27 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNB1 MUTATED      0    6
  KPNB1 WILD-TYPE   27  152
        clus
vv       KPNB1 MUTATED KPNB1 WILD-TYPE
  FEMALE             0              27
  MALE               6             152
[1] 2 2
[1] FALSE
D40V8, binary
                 cls
clus                0   1
  KPNB1 MUTATED     4   2
  KPNB1 WILD-TYPE 120  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNB1 MUTATED      4    2
  KPNB1 WILD-TYPE  120   41
     clus
vv    KPNB1 MUTATED KPNB1 WILD-TYPE
  NO              4             120
  YES             2              41
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, binary
                 cls
clus               0  1
  KPNB1 MUTATED    1  5
  KPNB1 WILD-TYPE 88 91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNB1 MUTATED      1    5
  KPNB1 WILD-TYPE   88   91
                                   clus
vv                                  KPNB1 MUTATED KPNB1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 1              88
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             5              91
[1] 2 2
[1] FALSE
D40V11, continuous
                 vv
clus               R0  R1  R2  RX
  KPNB1 MUTATED     5   1   0   0
  KPNB1 WILD-TYPE 132  12   2   7
D40V12, multiclass
    clus
vv   KPNB1 MUTATED KPNB1 WILD-TYPE
  R0             5             132
  R1             1              12
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KPNB1 MUTATED       4                         0     2
  KPNB1 WILD-TYPE    42                         5   112
D40V14, multiclass
                           clus
vv                          KPNB1 MUTATED KPNB1 WILD-TYPE
  ASIAN                                 4              42
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             112
[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"
D40V15, binary
                 cls
clus               0  1
  KPNB1 MUTATED    0  4
  KPNB1 WILD-TYPE  6 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNB1 MUTATED      0    4
  KPNB1 WILD-TYPE    6   84
                        clus
vv                       KPNB1 MUTATED KPNB1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4              84
[1] 2 2
[1] FALSE

Clustering(41) Variable = ZBED4 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  ZBED4 MUTATED     4   1
  ZBED4 WILD-TYPE 104  76
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              5             180 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              1              76 
$`ZBED4 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NN TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A5U7 
        4.31         5.49        15.35        12.62        25.25 

$`ZBED4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       12.33        13.38        13.15        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  ZBED4 MUTATED ZBED4 WILD-TYPE 
           4.31            0.13 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
          25.25          122.10 
  ZBED4 MUTATED ZBED4 WILD-TYPE 
         12.620          13.165 
[1] "4.3 - 25.2 (12.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.5"
D41V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBED4 MUTATED         0        0        0        0         3         1
  ZBED4 WILD-TYPE       8        5        6        1        44        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZBED4 MUTATED           1          0          0          0        0         0
  ZBED4 WILD-TYPE        25         14          9          7        5         4
D41V3, multiclass
            clus
vv           ZBED4 MUTATED ZBED4 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              3              44
  STAGE IIB              1              30
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  ZBED4 MUTATED       0  1  4  0
  ZBED4 WILD-TYPE    32 42 84  5
D41V4, multiclass
       clus
vv      ZBED4 MUTATED ZBED4 WILD-TYPE
  T0+T1             0              32
  T2                1              42
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ZBED4 MUTATED    4  1  0  0
  ZBED4 WILD-TYPE 73 68 12  8
D41V5, multiclass
    clus
vv   ZBED4 MUTATED ZBED4 WILD-TYPE
  N0             4              73
  N1             1              68
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                 cls
clus                0   1
  ZBED4 MUTATED     4   0
  ZBED4 WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      4    0
  ZBED4 WILD-TYPE  132    9
   clus
vv  ZBED4 MUTATED ZBED4 WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  ZBED4 MUTATED     0   5
  ZBED4 WILD-TYPE  27 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      0    5
  ZBED4 WILD-TYPE   27  153
        clus
vv       ZBED4 MUTATED ZBED4 WILD-TYPE
  FEMALE             0              27
  MALE               5             153
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus                0   1
  ZBED4 MUTATED     2   2
  ZBED4 WILD-TYPE 122  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      2    2
  ZBED4 WILD-TYPE  122   41
     clus
vv    ZBED4 MUTATED ZBED4 WILD-TYPE
  NO              2             122
  YES             2              41
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, binary
                 cls
clus               0  1
  ZBED4 MUTATED    1  4
  ZBED4 WILD-TYPE 88 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      1    4
  ZBED4 WILD-TYPE   88   92
                                   clus
vv                                  ZBED4 MUTATED ZBED4 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 1              88
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             4              92
[1] 2 2
[1] FALSE
D41V11, continuous
                 vv
clus               R0  R1  R2  RX
  ZBED4 MUTATED     4   0   0   1
  ZBED4 WILD-TYPE 133  13   2   6
D41V12, multiclass
    clus
vv   ZBED4 MUTATED ZBED4 WILD-TYPE
  R0             4             133
  R1             0              13
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, continuous
[1] "Remove cluster labels:" "ZBED4 MUTATED"         
clus
  ZBED4 MUTATED ZBED4 WILD-TYPE 
              2             133 
     TCGA-IC-A6RF      TCGA-JY-A6FB      TCGA-JY-A938      TCGA-L5-A43I 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A43M      TCGA-L5-A4OE      TCGA-L5-A4OG      TCGA-L5-A4OI 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-S8-A6BV      TCGA-2H-A9GF      TCGA-2H-A9GG 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-2H-A9GH      TCGA-2H-A9GI      TCGA-2H-A9GJ      TCGA-2H-A9GK 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-2H-A9GL      TCGA-2H-A9GM      TCGA-2H-A9GN      TCGA-2H-A9GO 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-2H-A9GQ      TCGA-2H-A9GR      TCGA-IC-A6RE      TCGA-IG-A3I8 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QS      TCGA-IG-A4QT 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A51D      TCGA-IG-A5B8      TCGA-IG-A5S3 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-IG-A625      TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97I 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-JY-A6F8      TCGA-JY-A6FA      TCGA-JY-A6FD      TCGA-JY-A6FE 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-JY-A939      TCGA-JY-A93C 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-JY-A93D      TCGA-JY-A93E      TCGA-JY-A93F      TCGA-L5-A43C 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OF      TCGA-L5-A4OH 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A4OJ      TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OR      TCGA-L5-A4OS 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A88W      TCGA-L5-A88Z 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A891      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A8NH      TCGA-L5-A8NI      TCGA-L5-A8NJ      TCGA-L5-A8NK 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A8NL      TCGA-L5-A8NM      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NV      TCGA-L5-A8NW      TCGA-L7-A6VZ 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49R      TCGA-LN-A49W      TCGA-LN-A4A3 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4MQ      TCGA-LN-A5U5      TCGA-LN-A5U6 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-LN-A7HY      TCGA-LN-A8I0      TCGA-LN-A9FR      TCGA-M9-A5M8 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-Q9-A6FW      TCGA-RE-A7BO      TCGA-S8-A6BW      TCGA-V5-A7RB 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-V5-A7RE      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE      TCGA-Z6-AAPN 
"ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" "ZBED4 WILD-TYPE" 
     TCGA-ZR-A9CJ 
"ZBED4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBED4 MUTATED       3                         0     2
  ZBED4 WILD-TYPE    43                         5   112
D41V14, multiclass
                           clus
vv                          ZBED4 MUTATED ZBED4 WILD-TYPE
  ASIAN                                 3              43
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             112
[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"
D41V15, binary
                 cls
clus               0  1
  ZBED4 MUTATED    0  3
  ZBED4 WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBED4 MUTATED      0    3
  ZBED4 WILD-TYPE    6   85
                        clus
vv                       ZBED4 MUTATED ZBED4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(42) Variable = NAA16 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  NAA16 MUTATED     4   2
  NAA16 WILD-TYPE 104  75
  NAA16 MUTATED NAA16 WILD-TYPE 
              6             179 
  NAA16 MUTATED NAA16 WILD-TYPE 
              2              75 
$`NAA16 MUTATED`
TCGA-L5-A88T TCGA-IC-A6RE TCGA-L5-A4OX TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-VR-A8ER 
       22.82         7.69         7.43        12.33         7.82        12.43 

$`NAA16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  NAA16 MUTATED NAA16 WILD-TYPE 
           7.43            0.13 
  NAA16 MUTATED NAA16 WILD-TYPE 
          22.82          122.10 
  NAA16 MUTATED NAA16 WILD-TYPE 
         10.075          13.180 
[1] "7.4 - 22.8 (10.1)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D42V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA16 MUTATED         0        0        0        0         0         4
  NAA16 WILD-TYPE       8        5        6        1        47        27
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA16 MUTATED           1          0          1          0        0         0
  NAA16 WILD-TYPE        25         14          8          7        5         4
D42V3, multiclass
            clus
vv           NAA16 MUTATED NAA16 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              0              47
  STAGE IIB              4              27
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             1               8
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  NAA16 MUTATED       1  3  1  1
  NAA16 WILD-TYPE    31 40 87  4
D42V4, multiclass
       clus
vv      NAA16 MUTATED NAA16 WILD-TYPE
  T0+T1             1              31
  T2                3              40
  T3                1              87
  T4                1               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  NAA16 MUTATED    0  5  1  0
  NAA16 WILD-TYPE 77 64 11  8
D42V5, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  N0             0              77
  N1             5              64
  N2             1              11
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                 cls
clus                0   1
  NAA16 MUTATED     6   0
  NAA16 WILD-TYPE 130   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      6    0
  NAA16 WILD-TYPE  130    9
   clus
vv  NAA16 MUTATED NAA16 WILD-TYPE
  0             6             130
  1             0               9
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  NAA16 MUTATED     0   6
  NAA16 WILD-TYPE  27 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      0    6
  NAA16 WILD-TYPE   27  152
        clus
vv       NAA16 MUTATED NAA16 WILD-TYPE
  FEMALE             0              27
  MALE               6             152
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus                0   1
  NAA16 MUTATED     4   2
  NAA16 WILD-TYPE 120  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      4    2
  NAA16 WILD-TYPE  120   41
     clus
vv    NAA16 MUTATED NAA16 WILD-TYPE
  NO              4             120
  YES             2              41
[1] 2 2
[1] FALSE
D42V9, continuous
[1] "Remove cluster labels:" "NAA16 MUTATED"         
clus
  NAA16 MUTATED NAA16 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
D42V10, binary
                 cls
clus               0  1
  NAA16 MUTATED    4  2
  NAA16 WILD-TYPE 85 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      4    2
  NAA16 WILD-TYPE   85   94
                                   clus
vv                                  NAA16 MUTATED NAA16 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 4              85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D42V11, continuous
                 vv
clus               R0  R1  R2  RX
  NAA16 MUTATED     4   1   0   1
  NAA16 WILD-TYPE 133  12   2   6
D42V12, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  R0             4             133
  R1             1              12
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA16 MUTATED       1                         0     4
  NAA16 WILD-TYPE    45                         5   110
D42V14, multiclass
                           clus
vv                          NAA16 MUTATED NAA16 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[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"
D42V15, binary
                 cls
clus               0  1
  NAA16 MUTATED    0  3
  NAA16 WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      0    3
  NAA16 WILD-TYPE    6   85
                        clus
vv                       NAA16 MUTATED NAA16 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(43) Variable = CNNM2 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  CNNM2 MUTATED     6   1
  CNNM2 WILD-TYPE 102  76
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              7             178 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              1              76 
$`CNNM2 MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
       19.99         7.69         7.40        55.50         2.66        16.47 
TCGA-LN-A7HX 
       12.23 

$`CNNM2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        3.02        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  CNNM2 MUTATED CNNM2 WILD-TYPE 
           2.66            0.13 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
           55.5           122.1 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
         12.230          13.165 
[1] "2.7 - 55.5 (12.2)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "2.9"
D43V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNNM2 MUTATED         0        0        0        0         2         2
  CNNM2 WILD-TYPE       8        5        6        1        45        29
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNNM2 MUTATED           1          0          0          1        0         1
  CNNM2 WILD-TYPE        25         14          9          6        5         3
D43V3, multiclass
            clus
vv           CNNM2 MUTATED CNNM2 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              2              45
  STAGE IIB              2              29
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  CNNM2 MUTATED       3  2  2  0
  CNNM2 WILD-TYPE    29 41 86  5
D43V4, multiclass
       clus
vv      CNNM2 MUTATED CNNM2 WILD-TYPE
  T0+T1             3              29
  T2                2              41
  T3                2              86
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CNNM2 MUTATED    2  4  0  1
  CNNM2 WILD-TYPE 75 65 12  7
D43V5, multiclass
    clus
vv   CNNM2 MUTATED CNNM2 WILD-TYPE
  N0             2              75
  N1             4              65
  N2             0              12
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                 cls
clus                0   1
  CNNM2 MUTATED     5   1
  CNNM2 WILD-TYPE 131   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      5    1
  CNNM2 WILD-TYPE  131    8
   clus
vv  CNNM2 MUTATED CNNM2 WILD-TYPE
  0             5             131
  1             1               8
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  CNNM2 MUTATED     1   6
  CNNM2 WILD-TYPE  26 152
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      1    6
  CNNM2 WILD-TYPE   26  152
        clus
vv       CNNM2 MUTATED CNNM2 WILD-TYPE
  FEMALE             1              26
  MALE               6             152
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus                0   1
  CNNM2 MUTATED     6   1
  CNNM2 WILD-TYPE 118  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      6    1
  CNNM2 WILD-TYPE  118   42
     clus
vv    CNNM2 MUTATED CNNM2 WILD-TYPE
  NO              6             118
  YES             1              42
[1] 2 2
[1] FALSE
D43V9, continuous
[1] "Remove cluster labels:" "CNNM2 MUTATED"         
clus
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
D43V10, binary
                 cls
clus               0  1
  CNNM2 MUTATED    5  2
  CNNM2 WILD-TYPE 84 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      5    2
  CNNM2 WILD-TYPE   84   94
                                   clus
vv                                  CNNM2 MUTATED CNNM2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 5              84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D43V11, continuous
                 vv
clus               R0  R1  R2  RX
  CNNM2 MUTATED     7   0   0   0
  CNNM2 WILD-TYPE 130  13   2   7
D43V12, multiclass
    clus
vv   CNNM2 MUTATED CNNM2 WILD-TYPE
  R0             7             130
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNNM2 MUTATED       1                         0     6
  CNNM2 WILD-TYPE    45                         5   108
D43V14, multiclass
                           clus
vv                          CNNM2 MUTATED CNNM2 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                 cls
clus               0  1
  CNNM2 MUTATED    0  2
  CNNM2 WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      0    2
  CNNM2 WILD-TYPE    6   86
                        clus
vv                       CNNM2 MUTATED CNNM2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(44) Variable = HLA-B MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED     6   1
  HLA-B WILD-TYPE 102  76
  HLA-B MUTATED HLA-B WILD-TYPE 
              7             178 
  HLA-B MUTATED HLA-B WILD-TYPE 
              1              76 
$`HLA-B MUTATED`
TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A4OP TCGA-L5-A8NJ TCGA-V5-AASX TCGA-VR-A8EP 
       41.52        24.03         7.17        16.47         8.98        27.09 
TCGA-Z6-AAPN 
        2.66 

$`HLA-B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         9.27        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        3.42         2.10         1.32        19.73 

  HLA-B MUTATED HLA-B WILD-TYPE 
           2.66            0.13 
  HLA-B MUTATED HLA-B WILD-TYPE 
          41.52          122.10 
  HLA-B MUTATED HLA-B WILD-TYPE 
         16.470          13.035 
[1] "2.7 - 41.5 (16.5)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "3.1"
D44V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-B MUTATED         0        1        1        0         1         0
  HLA-B WILD-TYPE       8        4        5        1        46        31
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-B MUTATED           2          0          1          0        0         0
  HLA-B WILD-TYPE        24         14          8          7        5         4
D44V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0               8
  STAGE IA               1               4
  STAGE IB               1               5
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              0              31
  STAGE III              2              24
  STAGE IIIA             0              14
  STAGE IIIB             1               8
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  HLA-B MUTATED       1  1  4  0
  HLA-B WILD-TYPE    31 42 84  5
D44V4, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T0+T1             1              31
  T2                1              42
  T3                4              84
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  HLA-B MUTATED    3  2  1  0
  HLA-B WILD-TYPE 74 67 11  8
D44V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0             3              74
  N1             2              67
  N2             1              11
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                 cls
clus                0   1
  HLA-B MUTATED     5   0
  HLA-B WILD-TYPE 131   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      5    0
  HLA-B WILD-TYPE  131    9
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             5             131
  1             0               9
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     2   5
  HLA-B WILD-TYPE  25 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      2    5
  HLA-B WILD-TYPE   25  153
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             2              25
  MALE               5             153
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus                0   1
  HLA-B MUTATED     5   0
  HLA-B WILD-TYPE 119  43
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      5    0
  HLA-B WILD-TYPE  119   43
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              5             119
  YES             0              43
[1] 2 2
[1] FALSE
D44V9, continuous
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EQ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
D44V10, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  4
  HLA-B WILD-TYPE 86 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    4
  HLA-B WILD-TYPE   86   92
                                   clus
vv                                  HLA-B MUTATED HLA-B WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 3              86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             4              92
[1] 2 2
[1] FALSE
D44V11, continuous
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     6   0   0   0
  HLA-B WILD-TYPE 131  13   2   7
D44V12, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             6             131
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       0                         0     7
  HLA-B WILD-TYPE    46                         5   107
D44V14, multiclass
                           clus
vv                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                 0              46
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[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"
D44V15, binary
                 cls
clus               0  1
  HLA-B MUTATED    0  2
  HLA-B WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0    2
  HLA-B WILD-TYPE    6   86
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(45) Variable = PLXNB2 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  PLXNB2 MUTATED    9  3
  PLXNB2 WILD-TYPE 99 74
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              12              173 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
               3               74 
$`PLXNB2 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GH TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-LN-A4A2 TCGA-LN-A5U6 
       19.99        31.27         6.28        21.01        12.49        12.33 
TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-R6-A6XQ TCGA-R6-A8WC TCGA-R6-A8WG 
       10.52        13.38        12.85         6.35         2.30        12.69 

$`PLXNB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ 
        5.16        20.02        25.78        20.05        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        12.33        13.22         4.47        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
            2.30             0.13 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
           31.27           122.10 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
           12.59            13.18 
[1] "2.3 - 31.3 (12.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D45V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLXNB2 MUTATED         1        1        0        0         4         2
  PLXNB2 WILD-TYPE       7        4        6        1        43        29
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNB2 MUTATED           0          0          0          1        0
  PLXNB2 WILD-TYPE        26         14          9          6        5
                  vv
clus               STAGE IVA
  PLXNB2 MUTATED           0
  PLXNB2 WILD-TYPE         4
D45V3, multiclass
            clus
vv           PLXNB2 MUTATED PLXNB2 WILD-TYPE
  STAGE I                 1                7
  STAGE IA                1                4
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               4               43
  STAGE IIB               2               29
  STAGE III               0               26
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  PLXNB2 MUTATED       3  3  3  0
  PLXNB2 WILD-TYPE    29 40 85  5
D45V4, multiclass
       clus
vv      PLXNB2 MUTATED PLXNB2 WILD-TYPE
  T0+T1              3               29
  T2                 3               40
  T3                 3               85
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PLXNB2 MUTATED    6  2  0  1
  PLXNB2 WILD-TYPE 71 67 12  7
D45V5, multiclass
    clus
vv   PLXNB2 MUTATED PLXNB2 WILD-TYPE
  N0              6               71
  N1              2               67
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED     8   0
  PLXNB2 WILD-TYPE 128   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      8    0
  PLXNB2 WILD-TYPE  128    9
   clus
vv  PLXNB2 MUTATED PLXNB2 WILD-TYPE
  0              8              128
  1              0                9
[1] 2 2
[1] FALSE
D45V7, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED     1  11
  PLXNB2 WILD-TYPE  26 147
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      1   11
  PLXNB2 WILD-TYPE   26  147
        clus
vv       PLXNB2 MUTATED PLXNB2 WILD-TYPE
  FEMALE              1               26
  MALE               11              147
[1] 2 2
[1] FALSE
D45V8, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED     7   4
  PLXNB2 WILD-TYPE 117  39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      7    4
  PLXNB2 WILD-TYPE  117   39
     clus
vv    PLXNB2 MUTATED PLXNB2 WILD-TYPE
  NO               7              117
  YES              4               39
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, binary
                  cls
clus                0  1
  PLXNB2 MUTATED    6  6
  PLXNB2 WILD-TYPE 83 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      6    6
  PLXNB2 WILD-TYPE   83   90
                                   clus
vv                                  PLXNB2 MUTATED PLXNB2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  6               83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              6               90
[1] 2 2
[1] FALSE
D45V11, continuous
                  vv
clus                R0  R1  R2  RX
  PLXNB2 MUTATED     8   0   0   0
  PLXNB2 WILD-TYPE 129  13   2   7
D45V12, multiclass
    clus
vv   PLXNB2 MUTATED PLXNB2 WILD-TYPE
  R0              8              129
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLXNB2 MUTATED       5                         0     6
  PLXNB2 WILD-TYPE    41                         5   108
D45V14, multiclass
                           clus
vv                          PLXNB2 MUTATED PLXNB2 WILD-TYPE
  ASIAN                                  5               41
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                  cls
clus                0  1
  PLXNB2 MUTATED    1  8
  PLXNB2 WILD-TYPE  5 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      1    8
  PLXNB2 WILD-TYPE    5   80
                        clus
vv                       PLXNB2 MUTATED PLXNB2 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              8               80
[1] 2 2
[1] FALSE

Clustering(46) Variable = PTEN MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     6   1
  PTEN WILD-TYPE 102  76
  PTEN MUTATED PTEN WILD-TYPE 
             7            178 
  PTEN MUTATED PTEN WILD-TYPE 
             1             76 
$`PTEN MUTATED`
TCGA-JY-A93F TCGA-L5-A88V TCGA-L5-A8NM TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV 
       24.03         2.60         7.76        12.33        13.22        10.52 
TCGA-VR-A8EP 
       27.09 

$`PTEN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        15.52        11.54         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  PTEN MUTATED PTEN WILD-TYPE 
          2.60           0.13 
  PTEN MUTATED PTEN WILD-TYPE 
         27.09         122.10 
  PTEN MUTATED PTEN WILD-TYPE 
        12.330         13.165 
[1] "2.6 - 27.1 (12.3)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "2.4"
D46V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTEN MUTATED         0        0        1        0         2         1
  PTEN WILD-TYPE       8        5        5        1        45        30
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED           2          0          1          0        0         0
  PTEN WILD-TYPE        24         14          8          7        5         4
D46V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               0              8
  STAGE IA              0              5
  STAGE IB              1              5
  STAGE II              0              1
  STAGE IIA             2             45
  STAGE IIB             1             30
  STAGE III             2             24
  STAGE IIIA            0             14
  STAGE IIIB            1              8
  STAGE IIIC            0              7
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  PTEN MUTATED       0  4  3  0
  PTEN WILD-TYPE    32 39 85  5
D46V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            0             32
  T2               4             39
  T3               3             85
  T4               0              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  PTEN MUTATED    3  3  1  0
  PTEN WILD-TYPE 74 66 11  8
D46V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0            3             74
  N1            3             66
  N2            1             11
  N3            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                cls
clus               0   1
  PTEN MUTATED     6   0
  PTEN WILD-TYPE 130   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6    0
  PTEN WILD-TYPE  130    9
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            6            130
  1            0              9
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  PTEN MUTATED     2   5
  PTEN WILD-TYPE  25 153
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2    5
  PTEN WILD-TYPE   25  153
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            2             25
  MALE              5            153
[1] 2 2
[1] FALSE
D46V8, binary
                cls
clus               0   1
  PTEN MUTATED     6   1
  PTEN WILD-TYPE 118  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6    1
  PTEN WILD-TYPE  118   42
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             6            118
  YES            1             42
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, binary
                cls
clus              0  1
  PTEN MUTATED    2  5
  PTEN WILD-TYPE 87 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2    5
  PTEN WILD-TYPE   87   91
                                   clus
vv                                  PTEN MUTATED PTEN WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                2             87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            5             91
[1] 2 2
[1] FALSE
D46V11, continuous
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     7   0   0   0
  PTEN WILD-TYPE 130  13   2   7
D46V12, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            7            130
  R1            0             13
  R2            0              2
  RX            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       3                         0     4
  PTEN WILD-TYPE    43                         5   110
D46V14, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                3             43
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[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"
D46V15, binary
                cls
clus              0  1
  PTEN MUTATED    0  3
  PTEN WILD-TYPE  6 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    3
  PTEN WILD-TYPE    6   85
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3             85
[1] 2 2
[1] FALSE

Clustering(47) Variable = CPT1B MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  CPT1B MUTATED     4   1
  CPT1B WILD-TYPE 104  76
  CPT1B MUTATED CPT1B WILD-TYPE 
              5             180 
  CPT1B MUTATED CPT1B WILD-TYPE 
              1              76 
$`CPT1B MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NJ TCGA-LN-A8HZ TCGA-VR-AA4G TCGA-XP-A8T6 
       19.99        16.47        12.33        18.05        25.08 

$`CPT1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       46.19        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  CPT1B MUTATED CPT1B WILD-TYPE 
          12.33            0.13 
  CPT1B MUTATED CPT1B WILD-TYPE 
          25.08          122.10 
  CPT1B MUTATED CPT1B WILD-TYPE 
         18.050          12.885 
[1] "12.3 - 25.1 (18.1)" "0.1 - 122.1 (12.9)"
[1] "hr=" "2.2"
D47V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CPT1B MUTATED         0        0        0        0         1         1
  CPT1B WILD-TYPE       8        5        6        1        46        30
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPT1B MUTATED           1          1          0          1        0         0
  CPT1B WILD-TYPE        25         13          9          6        5         4
D47V3, multiclass
            clus
vv           CPT1B MUTATED CPT1B WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              1              46
  STAGE IIB              1              30
  STAGE III              1              25
  STAGE IIIA             1              13
  STAGE IIIB             0               9
  STAGE IIIC             1               6
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  CPT1B MUTATED       0  3  2  0
  CPT1B WILD-TYPE    32 40 86  5
D47V4, multiclass
       clus
vv      CPT1B MUTATED CPT1B WILD-TYPE
  T0+T1             0              32
  T2                3              40
  T3                2              86
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  CPT1B MUTATED    1  2  1  1
  CPT1B WILD-TYPE 76 67 11  7
D47V5, multiclass
    clus
vv   CPT1B MUTATED CPT1B WILD-TYPE
  N0             1              76
  N1             2              67
  N2             1              11
  N3             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                 cls
clus                0   1
  CPT1B MUTATED     4   0
  CPT1B WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      4    0
  CPT1B WILD-TYPE  132    9
   clus
vv  CPT1B MUTATED CPT1B WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  CPT1B MUTATED     1   4
  CPT1B WILD-TYPE  26 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      1    4
  CPT1B WILD-TYPE   26  154
        clus
vv       CPT1B MUTATED CPT1B WILD-TYPE
  FEMALE             1              26
  MALE               4             154
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  CPT1B MUTATED     4   1
  CPT1B WILD-TYPE 120  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      4    1
  CPT1B WILD-TYPE  120   42
     clus
vv    CPT1B MUTATED CPT1B WILD-TYPE
  NO              4             120
  YES             1              42
[1] 2 2
[1] FALSE
D47V9, continuous
[1] "Remove cluster labels:" "CPT1B MUTATED"         
clus
  CPT1B MUTATED CPT1B WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CPT1B WILD-TYPE" "CPT1B WILD-TYPE" 
D47V10, binary
                 cls
clus               0  1
  CPT1B MUTATED    2  3
  CPT1B WILD-TYPE 87 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      2    3
  CPT1B WILD-TYPE   87   93
                                   clus
vv                                  CPT1B MUTATED CPT1B WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 2              87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             3              93
[1] 2 2
[1] FALSE
D47V11, continuous
                 vv
clus               R0  R1  R2  RX
  CPT1B MUTATED     5   0   0   0
  CPT1B WILD-TYPE 132  13   2   7
D47V12, multiclass
    clus
vv   CPT1B MUTATED CPT1B WILD-TYPE
  R0             5             132
  R1             0              13
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPT1B MUTATED       1                         1     3
  CPT1B WILD-TYPE    45                         4   111
D47V14, multiclass
                           clus
vv                          CPT1B MUTATED CPT1B WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[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"
D47V15, binary
                 cls
clus               0  1
  CPT1B MUTATED    1  1
  CPT1B WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      1    1
  CPT1B WILD-TYPE    5   87
                        clus
vv                       CPT1B MUTATED CPT1B WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             1              87
[1] 2 2
[1] FALSE

Clustering(48) Variable = CAMTA1 MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  CAMTA1 MUTATED     5   4
  CAMTA1 WILD-TYPE 103  73
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
               9              176 
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
               4               73 
$`CAMTA1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NG TCGA-2H-A9GR TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-L5-A8NW 
       19.99        35.97        32.45        21.01         7.76        46.09 
TCGA-LN-A8HZ TCGA-VR-AA7D TCGA-Z6-A8JE 
       12.33         9.17         2.10 

$`CAMTA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
            2.10             0.13 
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
           46.09           122.10 
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
          19.990           13.035 
[1] "2.1 - 46.1 (20.0)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.1"
D48V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CAMTA1 MUTATED         1        0        1        0         2         1
  CAMTA1 WILD-TYPE       7        5        5        1        45        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMTA1 MUTATED           1          1          0          2        0
  CAMTA1 WILD-TYPE        25         13          9          5        5
                  vv
clus               STAGE IVA
  CAMTA1 MUTATED           0
  CAMTA1 WILD-TYPE         4
D48V3, multiclass
            clus
vv           CAMTA1 MUTATED CAMTA1 WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               2               45
  STAGE IIB               1               30
  STAGE III               1               25
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              2                5
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  CAMTA1 MUTATED       1  3  5  0
  CAMTA1 WILD-TYPE    31 40 83  5
D48V4, multiclass
       clus
vv      CAMTA1 MUTATED CAMTA1 WILD-TYPE
  T0+T1              1               31
  T2                 3               40
  T3                 5               83
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CAMTA1 MUTATED    3  4  0  2
  CAMTA1 WILD-TYPE 74 65 12  6
D48V5, multiclass
    clus
vv   CAMTA1 MUTATED CAMTA1 WILD-TYPE
  N0              3               74
  N1              4               65
  N2              0               12
  N3              2                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                  cls
clus                 0   1
  CAMTA1 MUTATED     8   0
  CAMTA1 WILD-TYPE 128   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA1 MUTATED      8    0
  CAMTA1 WILD-TYPE  128    9
   clus
vv  CAMTA1 MUTATED CAMTA1 WILD-TYPE
  0              8              128
  1              0                9
[1] 2 2
[1] FALSE
D48V7, binary
                  cls
clus                 0   1
  CAMTA1 MUTATED     2   7
  CAMTA1 WILD-TYPE  25 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA1 MUTATED      2    7
  CAMTA1 WILD-TYPE   25  151
        clus
vv       CAMTA1 MUTATED CAMTA1 WILD-TYPE
  FEMALE              2               25
  MALE                7              151
[1] 2 2
[1] FALSE
D48V8, binary
                  cls
clus                 0   1
  CAMTA1 MUTATED     7   2
  CAMTA1 WILD-TYPE 117  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA1 MUTATED      7    2
  CAMTA1 WILD-TYPE  117   41
     clus
vv    CAMTA1 MUTATED CAMTA1 WILD-TYPE
  NO               7              117
  YES              2               41
[1] 2 2
[1] FALSE
D48V9, continuous
[1] "Remove cluster labels:" "CAMTA1 MUTATED"        
clus
  CAMTA1 MUTATED CAMTA1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD 
"CAMTA1 WILD-TYPE" "CAMTA1 WILD-TYPE" 
D48V10, binary
                  cls
clus                0  1
  CAMTA1 MUTATED    6  3
  CAMTA1 WILD-TYPE 83 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA1 MUTATED      6    3
  CAMTA1 WILD-TYPE   83   93
                                   clus
vv                                  CAMTA1 MUTATED CAMTA1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  6               83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              3               93
[1] 2 2
[1] FALSE
D48V11, continuous
                  vv
clus                R0  R1  R2  RX
  CAMTA1 MUTATED     7   1   0   1
  CAMTA1 WILD-TYPE 130  12   2   6
D48V12, multiclass
    clus
vv   CAMTA1 MUTATED CAMTA1 WILD-TYPE
  R0              7              130
  R1              1               12
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CAMTA1 MUTATED       1                         0     6
  CAMTA1 WILD-TYPE    45                         5   108
D48V14, multiclass
                           clus
vv                          CAMTA1 MUTATED CAMTA1 WILD-TYPE
  ASIAN                                  1               45
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                  cls
clus                0  1
  CAMTA1 MUTATED    0  2
  CAMTA1 WILD-TYPE  6 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAMTA1 MUTATED      0    2
  CAMTA1 WILD-TYPE    6   86
                        clus
vv                       CAMTA1 MUTATED CAMTA1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              2               86
[1] 2 2
[1] FALSE

Clustering(49) Variable = OTUD7B MUTATION ANALYSIS
D49V1, survival
                  sevent
clus2                0   1
  OTUD7B MUTATED     5   2
  OTUD7B WILD-TYPE 103  75
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               7              178 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               2               75 
$`OTUD7B MUTATED`
TCGA-IG-A3YA TCGA-JY-A6F8 TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L7-A6VZ 
       20.78       122.10        13.55         7.76         8.71        10.36 
TCGA-V5-A7RC 
        3.42 

$`OTUD7B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.22         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.10         1.32         2.66        19.73 

  OTUD7B MUTATED OTUD7B WILD-TYPE 
            3.42             0.13 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
          122.10            83.24 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
          10.360           13.165 
[1] "3.4 - 122.1 (10.4)" "0.1 - 83.2 (13.2)" 
[1] "hr=" "1.9"
D49V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OTUD7B MUTATED         1        0        0        0         1         1
  OTUD7B WILD-TYPE       7        5        6        1        46        30
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OTUD7B MUTATED           1          1          0          1        0
  OTUD7B WILD-TYPE        25         13          9          6        5
                  vv
clus               STAGE IVA
  OTUD7B MUTATED           0
  OTUD7B WILD-TYPE         4
D49V3, multiclass
            clus
vv           OTUD7B MUTATED OTUD7B WILD-TYPE
  STAGE I                 1                7
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               1               46
  STAGE IIB               1               30
  STAGE III               1               25
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  OTUD7B MUTATED       1  1  3  1
  OTUD7B WILD-TYPE    31 42 85  4
D49V4, multiclass
       clus
vv      OTUD7B MUTATED OTUD7B WILD-TYPE
  T0+T1              1               31
  T2                 1               42
  T3                 3               85
  T4                 1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  OTUD7B MUTATED    3  2  0  1
  OTUD7B WILD-TYPE 74 67 12  7
D49V5, multiclass
    clus
vv   OTUD7B MUTATED OTUD7B WILD-TYPE
  N0              3               74
  N1              2               67
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                  cls
clus                 0   1
  OTUD7B MUTATED     5   0
  OTUD7B WILD-TYPE 131   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      5    0
  OTUD7B WILD-TYPE  131    9
   clus
vv  OTUD7B MUTATED OTUD7B WILD-TYPE
  0              5              131
  1              0                9
[1] 2 2
[1] FALSE
D49V7, binary
                  cls
clus                 0   1
  OTUD7B MUTATED     3   4
  OTUD7B WILD-TYPE  24 154
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      3    4
  OTUD7B WILD-TYPE   24  154
        clus
vv       OTUD7B MUTATED OTUD7B WILD-TYPE
  FEMALE              3               24
  MALE                4              154
[1] 2 2
[1] FALSE
D49V8, binary
                  cls
clus                 0   1
  OTUD7B MUTATED     4   2
  OTUD7B WILD-TYPE 120  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      4    2
  OTUD7B WILD-TYPE  120   41
     clus
vv    OTUD7B MUTATED OTUD7B WILD-TYPE
  NO               4              120
  YES              2               41
[1] 2 2
[1] FALSE
D49V9, continuous
[1] "Remove cluster labels:" "OTUD7B MUTATED"        
clus
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YB 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
D49V10, binary
                  cls
clus                0  1
  OTUD7B MUTATED    4  3
  OTUD7B WILD-TYPE 85 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      4    3
  OTUD7B WILD-TYPE   85   93
                                   clus
vv                                  OTUD7B MUTATED OTUD7B WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  4               85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              3               93
[1] 2 2
[1] FALSE
D49V11, continuous
                  vv
clus                R0  R1  R2  RX
  OTUD7B MUTATED     5   1   0   0
  OTUD7B WILD-TYPE 132  12   2   7
D49V12, multiclass
    clus
vv   OTUD7B MUTATED OTUD7B WILD-TYPE
  R0              5              132
  R1              1               12
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTUD7B MUTATED       0                         1     5
  OTUD7B WILD-TYPE    46                         4   109
D49V14, multiclass
                           clus
vv                          OTUD7B MUTATED OTUD7B WILD-TYPE
  ASIAN                                  0               46
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  5              109
[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"
D49V15, binary
                  cls
clus                0  1
  OTUD7B MUTATED    0  3
  OTUD7B WILD-TYPE  6 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      0    3
  OTUD7B WILD-TYPE    6   85
                        clus
vv                       OTUD7B MUTATED OTUD7B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              3               85
[1] 2 2
[1] FALSE

Clustering(50) Variable = ARRB1 MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2               0   1
  ARRB1 MUTATED     3   2
  ARRB1 WILD-TYPE 105  75
  ARRB1 MUTATED ARRB1 WILD-TYPE 
              5             180 
  ARRB1 MUTATED ARRB1 WILD-TYPE 
              2              75 
$`ARRB1 MUTATED`
TCGA-L5-A43H TCGA-L5-A8NW TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-V5-AASW 
        0.30        46.09        15.52        33.11         9.27 

$`ARRB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 

  ARRB1 MUTATED ARRB1 WILD-TYPE 
           0.30            0.13 
  ARRB1 MUTATED ARRB1 WILD-TYPE 
          46.09          122.10 
  ARRB1 MUTATED ARRB1 WILD-TYPE 
         15.520          13.035 
[1] "0.3 - 46.1 (15.5)"  "0.1 - 122.1 (13.0)"
[1] "hr=" "1.2"
D50V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARRB1 MUTATED         0        0        1        0         2         0
  ARRB1 WILD-TYPE       8        5        5        1        45        31
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARRB1 MUTATED           1          0          0          0        0         0
  ARRB1 WILD-TYPE        25         14          9          7        5         4
D50V3, multiclass
            clus
vv           ARRB1 MUTATED ARRB1 WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               1               5
  STAGE II               0               1
  STAGE IIA              2              45
  STAGE IIB              0              31
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  ARRB1 MUTATED       0  2  2  0
  ARRB1 WILD-TYPE    32 41 86  5
D50V4, multiclass
       clus
vv      ARRB1 MUTATED ARRB1 WILD-TYPE
  T0+T1             0              32
  T2                2              41
  T3                2              86
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ARRB1 MUTATED    2  2  0  0
  ARRB1 WILD-TYPE 75 67 12  8
D50V5, multiclass
    clus
vv   ARRB1 MUTATED ARRB1 WILD-TYPE
  N0             2              75
  N1             2              67
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                 cls
clus                0   1
  ARRB1 MUTATED     4   0
  ARRB1 WILD-TYPE 132   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARRB1 MUTATED      4    0
  ARRB1 WILD-TYPE  132    9
   clus
vv  ARRB1 MUTATED ARRB1 WILD-TYPE
  0             4             132
  1             0               9
[1] 2 2
[1] FALSE
D50V7, binary
                 cls
clus                0   1
  ARRB1 MUTATED     0   5
  ARRB1 WILD-TYPE  27 153
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARRB1 MUTATED      0    5
  ARRB1 WILD-TYPE   27  153
        clus
vv       ARRB1 MUTATED ARRB1 WILD-TYPE
  FEMALE             0              27
  MALE               5             153
[1] 2 2
[1] FALSE
D50V8, binary
                 cls
clus                0   1
  ARRB1 MUTATED     4   1
  ARRB1 WILD-TYPE 120  42
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARRB1 MUTATED      4    1
  ARRB1 WILD-TYPE  120   42
     clus
vv    ARRB1 MUTATED ARRB1 WILD-TYPE
  NO              4             120
  YES             1              42
[1] 2 2
[1] FALSE
D50V9, continuous
[1] "Remove cluster labels:" "ARRB1 MUTATED"         
clus
  ARRB1 MUTATED ARRB1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ARRB1 WILD-TYPE" "ARRB1 WILD-TYPE" 
D50V10, binary
                 cls
clus               0  1
  ARRB1 MUTATED    3  2
  ARRB1 WILD-TYPE 86 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARRB1 MUTATED      3    2
  ARRB1 WILD-TYPE   86   94
                                   clus
vv                                  ARRB1 MUTATED ARRB1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 3              86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             2              94
[1] 2 2
[1] FALSE
D50V11, continuous
                 vv
clus               R0  R1  R2  RX
  ARRB1 MUTATED     3   1   0   0
  ARRB1 WILD-TYPE 134  12   2   7
D50V12, multiclass
    clus
vv   ARRB1 MUTATED ARRB1 WILD-TYPE
  R0             3             134
  R1             1              12
  R2             0               2
  RX             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARRB1 MUTATED       1                         0     3
  ARRB1 WILD-TYPE    45                         5   111
D50V14, multiclass
                           clus
vv                          ARRB1 MUTATED ARRB1 WILD-TYPE
  ASIAN                                 1              45
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[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"
D50V15, binary
                 cls
clus               0  1
  ARRB1 MUTATED    0  2
  ARRB1 WILD-TYPE  6 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARRB1 MUTATED      0    2
  ARRB1 WILD-TYPE    6   86
                        clus
vv                       ARRB1 MUTATED ARRB1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             2              86
[1] 2 2
[1] FALSE

Clustering(51) Variable = KIAA1704 MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  KIAA1704 MUTATED     1   2
  KIAA1704 WILD-TYPE 107  75
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 3                182 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 2                 75 
$`KIAA1704 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-VR-A8EW 
       19.99         7.76         8.12 

$`KIAA1704 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        2.66        19.73 

  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
              7.76               0.13 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
             19.99             122.10 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
             8.120             13.165 
[1] "7.8 - 20.0 (8.1)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2.3"
D51V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1704 MUTATED         0        0        0        0         0         1
  KIAA1704 WILD-TYPE       8        5        6        1        47        30
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1704 MUTATED           0          0          1          1        0
  KIAA1704 WILD-TYPE        26         14          8          6        5
                    vv
clus                 STAGE IVA
  KIAA1704 MUTATED           0
  KIAA1704 WILD-TYPE         4
D51V3, multiclass
            clus
vv           KIAA1704 MUTATED KIAA1704 WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  0                  6
  STAGE II                  0                  1
  STAGE IIA                 0                 47
  STAGE IIB                 1                 30
  STAGE III                 0                 26
  STAGE IIIA                0                 14
  STAGE IIIB                1                  8
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  KIAA1704 MUTATED       0  1  2  0
  KIAA1704 WILD-TYPE    32 42 86  5
D51V4, multiclass
       clus
vv      KIAA1704 MUTATED KIAA1704 WILD-TYPE
  T0+T1                0                 32
  T2                   1                 42
  T3                   2                 86
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1704 MUTATED    0  1  1  1
  KIAA1704 WILD-TYPE 77 68 11  7
D51V5, multiclass
    clus
vv   KIAA1704 MUTATED KIAA1704 WILD-TYPE
  N0                0                 77
  N1                1                 68
  N2                1                 11
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     2   0
  KIAA1704 WILD-TYPE 134   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      2    0
  KIAA1704 WILD-TYPE  134    9
   clus
vv  KIAA1704 MUTATED KIAA1704 WILD-TYPE
  0                2                134
  1                0                  9
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     1   2
  KIAA1704 WILD-TYPE  26 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      1    2
  KIAA1704 WILD-TYPE   26  156
        clus
vv       KIAA1704 MUTATED KIAA1704 WILD-TYPE
  FEMALE                1                 26
  MALE                  2                156
[1] 2 2
[1] FALSE
D51V8, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     3   0
  KIAA1704 WILD-TYPE 121  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      3    0
  KIAA1704 WILD-TYPE  121   43
     clus
vv    KIAA1704 MUTATED KIAA1704 WILD-TYPE
  NO                 3                121
  YES                0                 43
[1] 2 2
[1] FALSE
D51V9, continuous
[1] "Remove cluster labels:" "KIAA1704 MUTATED"      
clus
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1704 WILD-TYPE" 
D51V10, binary
                    cls
clus                  0  1
  KIAA1704 MUTATED    2  1
  KIAA1704 WILD-TYPE 87 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      2    1
  KIAA1704 WILD-TYPE   87   95
                                   clus
vv                                  KIAA1704 MUTATED KIAA1704 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    2                 87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                1                 95
[1] 2 2
[1] FALSE
D51V11, continuous
[1] "Remove cluster labels:" "KIAA1704 MUTATED"      
clus
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
                    vv
clus                  R0  R1  R2  RX
  KIAA1704 MUTATED     3   0   0   0
  KIAA1704 WILD-TYPE 134  13   2   7
D51V12, multiclass
    clus
vv   KIAA1704 MUTATED KIAA1704 WILD-TYPE
  R0                3                134
  R1                0                 13
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1704 MUTATED       1                         0     2
  KIAA1704 WILD-TYPE    45                         5   112
D51V14, multiclass
                           clus
vv                          KIAA1704 MUTATED KIAA1704 WILD-TYPE
  ASIAN                                    1                 45
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    2                112
[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"
D51V15, binary
                    cls
clus                  0  1
  KIAA1704 MUTATED    0  0
  KIAA1704 WILD-TYPE  6 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      0    0
  KIAA1704 WILD-TYPE    6   88

Clustering(52) Variable = RNF169 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  RNF169 MUTATED     4   2
  RNF169 WILD-TYPE 104  75
  RNF169 MUTATED RNF169 WILD-TYPE 
               6              179 
  RNF169 MUTATED RNF169 WILD-TYPE 
               2               75 
$`RNF169 MUTATED`
TCGA-IC-A6RE TCGA-L5-A8NH TCGA-L5-A8NS TCGA-LN-A49R TCGA-LN-A4A9 TCGA-V5-AASW 
        7.69        12.92        13.41        13.38        11.54         9.27 

$`RNF169 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        3.42         2.10         1.32         2.66        19.73 

  RNF169 MUTATED RNF169 WILD-TYPE 
            7.69             0.13 
  RNF169 MUTATED RNF169 WILD-TYPE 
           13.41           122.10 
  RNF169 MUTATED RNF169 WILD-TYPE 
           12.23            13.18 
[1] "7.7 - 13.4 (12.2)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.3"
D52V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF169 MUTATED         0        0        0        0         1         2
  RNF169 WILD-TYPE       8        5        6        1        46        29
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF169 MUTATED           1          0          0          0        1
  RNF169 WILD-TYPE        25         14          9          7        4
                  vv
clus               STAGE IVA
  RNF169 MUTATED           0
  RNF169 WILD-TYPE         4
D52V3, multiclass
            clus
vv           RNF169 MUTATED RNF169 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               1               46
  STAGE IIB               2               29
  STAGE III               1               25
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              0                7
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  RNF169 MUTATED       2  1  2  0
  RNF169 WILD-TYPE    30 42 86  5
D52V4, multiclass
       clus
vv      RNF169 MUTATED RNF169 WILD-TYPE
  T0+T1              2               30
  T2                 1               42
  T3                 2               86
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RNF169 MUTATED    3  2  0  0
  RNF169 WILD-TYPE 74 67 12  8
D52V5, multiclass
    clus
vv   RNF169 MUTATED RNF169 WILD-TYPE
  N0              3               74
  N1              2               67
  N2              0               12
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                  cls
clus                 0   1
  RNF169 MUTATED     4   1
  RNF169 WILD-TYPE 132   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF169 MUTATED      4    1
  RNF169 WILD-TYPE  132    8
   clus
vv  RNF169 MUTATED RNF169 WILD-TYPE
  0              4              132
  1              1                8
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  RNF169 MUTATED     0   6
  RNF169 WILD-TYPE  27 152
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF169 MUTATED      0    6
  RNF169 WILD-TYPE   27  152
        clus
vv       RNF169 MUTATED RNF169 WILD-TYPE
  FEMALE              0               27
  MALE                6              152
[1] 2 2
[1] FALSE
D52V8, binary
                  cls
clus                 0   1
  RNF169 MUTATED     2   3
  RNF169 WILD-TYPE 122  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF169 MUTATED      2    3
  RNF169 WILD-TYPE  122   40
     clus
vv    RNF169 MUTATED RNF169 WILD-TYPE
  NO               2              122
  YES              3               40
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, binary
                  cls
clus                0  1
  RNF169 MUTATED    4  2
  RNF169 WILD-TYPE 85 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF169 MUTATED      4    2
  RNF169 WILD-TYPE   85   94
                                   clus
vv                                  RNF169 MUTATED RNF169 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  4               85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              2               94
[1] 2 2
[1] FALSE
D52V11, continuous
                  vv
clus                R0  R1  R2  RX
  RNF169 MUTATED     5   0   0   0
  RNF169 WILD-TYPE 132  13   2   7
D52V12, multiclass
    clus
vv   RNF169 MUTATED RNF169 WILD-TYPE
  R0              5              132
  R1              0               13
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF169 MUTATED       2                         0     4
  RNF169 WILD-TYPE    44                         5   110
D52V14, multiclass
                           clus
vv                          RNF169 MUTATED RNF169 WILD-TYPE
  ASIAN                                  2               44
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[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"
D52V15, binary
                  cls
clus                0  1
  RNF169 MUTATED    0  4
  RNF169 WILD-TYPE  6 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF169 MUTATED      0    4
  RNF169 WILD-TYPE    6   84
                        clus
vv                       RNF169 MUTATED RNF169 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4               84
[1] 2 2
[1] FALSE

Clustering(53) Variable = RBPJL MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  RBPJL MUTATED     3   3
  RBPJL WILD-TYPE 105  74
  RBPJL MUTATED RBPJL WILD-TYPE 
              6             179 
  RBPJL MUTATED RBPJL WILD-TYPE 
              3              74 
$`RBPJL MUTATED`
TCGA-L5-A43J TCGA-L5-A8NM TCGA-LN-A7HV TCGA-LN-A9FP TCGA-VR-A8EQ TCGA-Z6-AAPN 
        4.31         7.76        10.52        12.03        22.82         2.66 

$`RBPJL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32        19.73 

  RBPJL MUTATED RBPJL WILD-TYPE 
           2.66            0.13 
  RBPJL MUTATED RBPJL WILD-TYPE 
          22.82          122.10 
  RBPJL MUTATED RBPJL WILD-TYPE 
           9.14           13.18 
[1] "2.7 - 22.8 (9.1)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2.2"
D53V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBPJL MUTATED         0        0        0        0         3         2
  RBPJL WILD-TYPE       8        5        6        1        44        29
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBPJL MUTATED           1          0          0          0        0         0
  RBPJL WILD-TYPE        25         14          9          7        5         4
D53V3, multiclass
            clus
vv           RBPJL MUTATED RBPJL WILD-TYPE
  STAGE I                0               8
  STAGE IA               0               5
  STAGE IB               0               6
  STAGE II               0               1
  STAGE IIA              3              44
  STAGE IIB              2              29
  STAGE III              1              25
  STAGE IIIA             0              14
  STAGE IIIB             0               9
  STAGE IIIC             0               7
  STAGE IV               0               5
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1 T2 T3 T4
  RBPJL MUTATED       0  3  3  0
  RBPJL WILD-TYPE    32 40 85  5
D53V4, multiclass
       clus
vv      RBPJL MUTATED RBPJL WILD-TYPE
  T0+T1             0              32
  T2                3              40
  T3                3              85
  T4                0               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RBPJL MUTATED    4  2  0  0
  RBPJL WILD-TYPE 73 67 12  8
D53V5, multiclass
    clus
vv   RBPJL MUTATED RBPJL WILD-TYPE
  N0             4              73
  N1             2              67
  N2             0              12
  N3             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                 cls
clus                0   1
  RBPJL MUTATED     5   0
  RBPJL WILD-TYPE 131   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPJL MUTATED      5    0
  RBPJL WILD-TYPE  131    9
   clus
vv  RBPJL MUTATED RBPJL WILD-TYPE
  0             5             131
  1             0               9
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus                0   1
  RBPJL MUTATED     2   4
  RBPJL WILD-TYPE  25 154
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPJL MUTATED      2    4
  RBPJL WILD-TYPE   25  154
        clus
vv       RBPJL MUTATED RBPJL WILD-TYPE
  FEMALE             2              25
  MALE               4             154
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus                0   1
  RBPJL MUTATED     2   3
  RBPJL WILD-TYPE 122  40
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPJL MUTATED      2    3
  RBPJL WILD-TYPE  122   40
     clus
vv    RBPJL MUTATED RBPJL WILD-TYPE
  NO              2             122
  YES             3              40
[1] 2 2
[1] FALSE
D53V9, continuous
[1] "Remove cluster labels:" "RBPJL MUTATED"         
clus
  RBPJL MUTATED RBPJL WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RBPJL WILD-TYPE" "RBPJL WILD-TYPE" 
D53V10, binary
                 cls
clus               0  1
  RBPJL MUTATED    2  4
  RBPJL WILD-TYPE 87 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPJL MUTATED      2    4
  RBPJL WILD-TYPE   87   92
                                   clus
vv                                  RBPJL MUTATED RBPJL WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 2              87
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             4              92
[1] 2 2
[1] FALSE
D53V11, continuous
                 vv
clus               R0  R1  R2  RX
  RBPJL MUTATED     5   0   0   1
  RBPJL WILD-TYPE 132  13   2   6
D53V12, multiclass
    clus
vv   RBPJL MUTATED RBPJL WILD-TYPE
  R0             5             132
  R1             0              13
  R2             0               2
  RX             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBPJL MUTATED       2                         0     4
  RBPJL WILD-TYPE    44                         5   110
D53V14, multiclass
                           clus
vv                          RBPJL MUTATED RBPJL WILD-TYPE
  ASIAN                                 2              44
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[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"
D53V15, binary
                 cls
clus               0  1
  RBPJL MUTATED    0  3
  RBPJL WILD-TYPE  6 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPJL MUTATED      0    3
  RBPJL WILD-TYPE    6   85
                        clus
vv                       RBPJL MUTATED RBPJL WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             3              85
[1] 2 2
[1] FALSE

Clustering(54) Variable = MGAT5B MUTATION ANALYSIS
D54V1, survival
                  sevent
clus2                0   1
  MGAT5B MUTATED     3   5
  MGAT5B WILD-TYPE 105  72
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               8              177 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
               5               72 
$`MGAT5B MUTATED`
TCGA-L5-A4OI TCGA-IG-A51D TCGA-JY-A6FE TCGA-L5-A8NM TCGA-LN-A9FR TCGA-R6-A6Y2 
       19.99        17.03         3.68         7.76        12.26         9.30 
TCGA-V5-A7RB TCGA-VR-A8EU 
        5.29        18.31 

$`MGAT5B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  MGAT5B MUTATED MGAT5B WILD-TYPE 
            3.68             0.13 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
           19.99           122.10 
  MGAT5B MUTATED MGAT5B WILD-TYPE 
           10.78            13.18 
[1] "3.7 - 20.0 (10.8)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "2.4"
D54V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGAT5B MUTATED         0        0        0        0         0         3
  MGAT5B WILD-TYPE       8        5        6        1        47        28
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGAT5B MUTATED           1          0          0          1        1
  MGAT5B WILD-TYPE        25         14          9          6        4
                  vv
clus               STAGE IVA
  MGAT5B MUTATED           0
  MGAT5B WILD-TYPE         4
D54V3, multiclass
            clus
vv           MGAT5B MUTATED MGAT5B WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               0               47
  STAGE IIB               3               28
  STAGE III               1               25
  STAGE IIIA              0               14
  STAGE IIIB              0                9
  STAGE IIIC              1                6
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  MGAT5B MUTATED       3  2  2  0
  MGAT5B WILD-TYPE    29 41 86  5
D54V4, multiclass
       clus
vv      MGAT5B MUTATED MGAT5B WILD-TYPE
  T0+T1              3               29
  T2                 2               41
  T3                 2               86
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  MGAT5B MUTATED    0  6  0  1
  MGAT5B WILD-TYPE 77 63 12  7
D54V5, multiclass
    clus
vv   MGAT5B MUTATED MGAT5B WILD-TYPE
  N0              0               77
  N1              6               63
  N2              0               12
  N3              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     4   1
  MGAT5B WILD-TYPE 132   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      4    1
  MGAT5B WILD-TYPE  132    8
   clus
vv  MGAT5B MUTATED MGAT5B WILD-TYPE
  0              4              132
  1              1                8
[1] 2 2
[1] FALSE
D54V7, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     1   7
  MGAT5B WILD-TYPE  26 151
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      1    7
  MGAT5B WILD-TYPE   26  151
        clus
vv       MGAT5B MUTATED MGAT5B WILD-TYPE
  FEMALE              1               26
  MALE                7              151
[1] 2 2
[1] FALSE
D54V8, binary
                  cls
clus                 0   1
  MGAT5B MUTATED     6   2
  MGAT5B WILD-TYPE 118  41
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      6    2
  MGAT5B WILD-TYPE  118   41
     clus
vv    MGAT5B MUTATED MGAT5B WILD-TYPE
  NO               6              118
  YES              2               41
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, binary
                  cls
clus                0  1
  MGAT5B MUTATED    4  4
  MGAT5B WILD-TYPE 85 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      4    4
  MGAT5B WILD-TYPE   85   92
                                   clus
vv                                  MGAT5B MUTATED MGAT5B WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  4               85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              4               92
[1] 2 2
[1] FALSE
D54V11, continuous
                  vv
clus                R0  R1  R2  RX
  MGAT5B MUTATED     6   0   0   1
  MGAT5B WILD-TYPE 131  13   2   6
D54V12, multiclass
    clus
vv   MGAT5B MUTATED MGAT5B WILD-TYPE
  R0              6              131
  R1              0               13
  R2              0                2
  RX              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MGAT5B MUTATED       1                         0     6
  MGAT5B WILD-TYPE    45                         5   108
D54V14, multiclass
                           clus
vv                          MGAT5B MUTATED MGAT5B WILD-TYPE
  ASIAN                                  1               45
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                  cls
clus                0  1
  MGAT5B MUTATED    2  2
  MGAT5B WILD-TYPE  4 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MGAT5B MUTATED      2    2
  MGAT5B WILD-TYPE    4   86
                        clus
vv                       MGAT5B MUTATED MGAT5B WILD-TYPE
  HISPANIC OR LATINO                  2                4
  NOT HISPANIC OR LATINO              2               86
[1] 2 2
[1] FALSE

Clustering(55) Variable = LRRC32 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  LRRC32 MUTATED     4   5
  LRRC32 WILD-TYPE 104  72
  LRRC32 MUTATED LRRC32 WILD-TYPE 
               9              176 
  LRRC32 MUTATED LRRC32 WILD-TYPE 
               5               72 
$`LRRC32 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-2H-A9GL TCGA-2H-A9GR TCGA-L5-A8NS TCGA-LN-A49N 
        4.31        24.00         5.92        32.45        13.41        12.43 
TCGA-R6-A6XQ TCGA-Z6-A8JE TCGA-Z6-AAPN 
        6.35         2.10         2.66 

$`LRRC32 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        7.63        13.94         8.94        16.24         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-ZR-A9CJ 
        1.32        19.73 

  LRRC32 MUTATED LRRC32 WILD-TYPE 
            2.10             0.13 
  LRRC32 MUTATED LRRC32 WILD-TYPE 
           32.45           122.10 
  LRRC32 MUTATED LRRC32 WILD-TYPE 
            6.35            13.18 
[1] "2.1 - 32.5 (6.3)"   "0.1 - 122.1 (13.2)"
[1] "hr=" "2.1"
D55V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRC32 MUTATED         0        0        0        0         2         3
  LRRC32 WILD-TYPE       8        5        6        1        45        28
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC32 MUTATED           1          1          1          0        0
  LRRC32 WILD-TYPE        25         13          8          7        5
                  vv
clus               STAGE IVA
  LRRC32 MUTATED           0
  LRRC32 WILD-TYPE         4
D55V3, multiclass
            clus
vv           LRRC32 MUTATED LRRC32 WILD-TYPE
  STAGE I                 0                8
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               2               45
  STAGE IIB               3               28
  STAGE III               1               25
  STAGE IIIA              1               13
  STAGE IIIB              1                8
  STAGE IIIC              0                7
  STAGE IV                0                5
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  LRRC32 MUTATED       0  1  7  0
  LRRC32 WILD-TYPE    32 42 81  5
D55V4, multiclass
       clus
vv      LRRC32 MUTATED LRRC32 WILD-TYPE
  T0+T1              0               32
  T2                 1               42
  T3                 7               81
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  LRRC32 MUTATED    4  3  1  0
  LRRC32 WILD-TYPE 73 66 11  8
D55V5, multiclass
    clus
vv   LRRC32 MUTATED LRRC32 WILD-TYPE
  N0              4               73
  N1              3               66
  N2              1               11
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                  cls
clus                 0   1
  LRRC32 MUTATED     6   0
  LRRC32 WILD-TYPE 130   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC32 MUTATED      6    0
  LRRC32 WILD-TYPE  130    9
   clus
vv  LRRC32 MUTATED LRRC32 WILD-TYPE
  0              6              130
  1              0                9
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  LRRC32 MUTATED     0   9
  LRRC32 WILD-TYPE  27 149
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC32 MUTATED      0    9
  LRRC32 WILD-TYPE   27  149
        clus
vv       LRRC32 MUTATED LRRC32 WILD-TYPE
  FEMALE              0               27
  MALE                9              149
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  LRRC32 MUTATED     7   1
  LRRC32 WILD-TYPE 117  42
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC32 MUTATED      7    1
  LRRC32 WILD-TYPE  117   42
     clus
vv    LRRC32 MUTATED LRRC32 WILD-TYPE
  NO               7              117
  YES              1               42
[1] 2 2
[1] FALSE
D55V9, continuous
[1] "Remove cluster labels:" "LRRC32 MUTATED"        
clus
  LRRC32 MUTATED LRRC32 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD 
"LRRC32 WILD-TYPE" "LRRC32 WILD-TYPE" 
D55V10, binary
                  cls
clus                0  1
  LRRC32 MUTATED    5  4
  LRRC32 WILD-TYPE 84 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC32 MUTATED      5    4
  LRRC32 WILD-TYPE   84   92
                                   clus
vv                                  LRRC32 MUTATED LRRC32 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                  5               84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              4               92
[1] 2 2
[1] FALSE
D55V11, continuous
                  vv
clus                R0  R1  R2  RX
  LRRC32 MUTATED     3   2   0   3
  LRRC32 WILD-TYPE 134  11   2   4
D55V12, multiclass
    clus
vv   LRRC32 MUTATED LRRC32 WILD-TYPE
  R0              3              134
  R1              2               11
  R2              0                2
  RX              3                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRRC32 MUTATED       1                         0     6
  LRRC32 WILD-TYPE    45                         5   108
D55V14, multiclass
                           clus
vv                          LRRC32 MUTATED LRRC32 WILD-TYPE
  ASIAN                                  1               45
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                  cls
clus                0  1
  LRRC32 MUTATED    0  4
  LRRC32 WILD-TYPE  6 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC32 MUTATED      0    4
  LRRC32 WILD-TYPE    6   84
                        clus
vv                       LRRC32 MUTATED LRRC32 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4               84
[1] 2 2
[1] FALSE

Clustering(56) Variable = TCHH MUTATION ANALYSIS
D56V1, survival
                sevent
clus2             0  1
  TCHH MUTATED   11  3
  TCHH WILD-TYPE 97 74
  TCHH MUTATED TCHH WILD-TYPE 
            14            171 
  TCHH MUTATED TCHH WILD-TYPE 
             3             74 
$`TCHH MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-JY-A93E TCGA-L5-A8NM TCGA-L5-A8NR TCGA-LN-A49P 
       34.85        19.99        25.22         7.76         8.71        12.33 
TCGA-LN-A4A4 TCGA-LN-A9FQ TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO 
       12.59        12.85         3.42        16.44        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER 
       27.09        12.43 

$`TCHH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00        20.38         5.29         9.27         8.98        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  TCHH MUTATED TCHH WILD-TYPE 
          3.42           0.13 
  TCHH MUTATED TCHH WILD-TYPE 
         34.85         122.10 
  TCHH MUTATED TCHH WILD-TYPE 
         14.10          13.15 
[1] "3.4 - 34.9 (14.1)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "2"  
D56V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCHH MUTATED         0        0        1        0         3         3
  TCHH WILD-TYPE       8        5        5        1        44        28
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCHH MUTATED           3          1          1          1        0         0
  TCHH WILD-TYPE        23         13          8          6        5         4
D56V3, multiclass
            clus
vv           TCHH MUTATED TCHH WILD-TYPE
  STAGE I               0              8
  STAGE IA              0              5
  STAGE IB              1              5
  STAGE II              0              1
  STAGE IIA             3             44
  STAGE IIB             3             28
  STAGE III             3             23
  STAGE IIIA            1             13
  STAGE IIIB            1              8
  STAGE IIIC            1              6
  STAGE IV              0              5
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  TCHH MUTATED       1  1 10  1
  TCHH WILD-TYPE    31 42 78  4
D56V4, multiclass
       clus
vv      TCHH MUTATED TCHH WILD-TYPE
  T0+T1            1             31
  T2               1             42
  T3              10             78
  T4               1              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TCHH MUTATED    6  5  1  1
  TCHH WILD-TYPE 71 64 11  7
D56V5, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  N0            6             71
  N1            5             64
  N2            1             11
  N3            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                cls
clus               0   1
  TCHH MUTATED    11   0
  TCHH WILD-TYPE 125   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED     11    0
  TCHH WILD-TYPE  125    9
   clus
vv  TCHH MUTATED TCHH WILD-TYPE
  0           11            125
  1            0              9
[1] 2 2
[1] FALSE
D56V7, binary
                cls
clus               0   1
  TCHH MUTATED     2  12
  TCHH WILD-TYPE  25 146
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      2   12
  TCHH WILD-TYPE   25  146
        clus
vv       TCHH MUTATED TCHH WILD-TYPE
  FEMALE            2             25
  MALE             12            146
[1] 2 2
[1] FALSE
D56V8, binary
                cls
clus               0   1
  TCHH MUTATED     7   7
  TCHH WILD-TYPE 117  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      7    7
  TCHH WILD-TYPE  117   36
     clus
vv    TCHH MUTATED TCHH WILD-TYPE
  NO             7            117
  YES            7             36
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, binary
                cls
clus              0  1
  TCHH MUTATED    6  8
  TCHH WILD-TYPE 83 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      6    8
  TCHH WILD-TYPE   83   88
                                   clus
vv                                  TCHH MUTATED TCHH WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                6             83
  ESOPHAGUS SQUAMOUS CELL CARCINOMA            8             88
[1] 2 2
[1] FALSE
D56V11, continuous
                vv
clus              R0  R1  R2  RX
  TCHH MUTATED    12   1   0   0
  TCHH WILD-TYPE 125  12   2   7
D56V12, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  R0           12            125
  R1            1             12
  R2            0              2
  RX            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCHH MUTATED       3                         2     7
  TCHH WILD-TYPE    43                         3   107
D56V14, multiclass
                           clus
vv                          TCHH MUTATED TCHH WILD-TYPE
  ASIAN                                3             43
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                                7            107
[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"
D56V15, binary
                cls
clus              0  1
  TCHH MUTATED    0  6
  TCHH WILD-TYPE  6 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      0    6
  TCHH WILD-TYPE    6   82
                        clus
vv                       TCHH MUTATED TCHH WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6             82
[1] 2 2
[1] FALSE

Clustering(57) Variable = SLC22A2 MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  SLC22A2 MUTATED     2   2
  SLC22A2 WILD-TYPE 106  75
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
                4               181 
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
                2                75 
$`SLC22A2 MUTATED`
TCGA-JY-A93C TCGA-L5-A8NH TCGA-LN-A9FP TCGA-VR-AA4D 
       23.18        12.92        12.03        46.19 

$`SLC22A2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       27.12         5.16        20.02        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ 
       19.73 

  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
            12.03              0.13 
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
            46.19            122.10 
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
            18.05             13.15 
[1] "12.0 - 46.2 (18.1)" "0.1 - 122.1 (13.2)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC22A2 MUTATED         0        0        0        0         1         1
  SLC22A2 WILD-TYPE       8        5        6        1        46        30
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A2 MUTATED           0          0          1          0        1
  SLC22A2 WILD-TYPE        26         14          8          7        4
                   vv
clus                STAGE IVA
  SLC22A2 MUTATED           0
  SLC22A2 WILD-TYPE         4
D57V3, multiclass
            clus
vv           SLC22A2 MUTATED SLC22A2 WILD-TYPE
  STAGE I                  0                 8
  STAGE IA                 0                 5
  STAGE IB                 0                 6
  STAGE II                 0                 1
  STAGE IIA                1                46
  STAGE IIB                1                30
  STAGE III                0                26
  STAGE IIIA               0                14
  STAGE IIIB               1                 8
  STAGE IIIC               0                 7
  STAGE IV                 1                 4
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  SLC22A2 MUTATED       2  1  1  0
  SLC22A2 WILD-TYPE    30 42 87  5
D57V4, multiclass
       clus
vv      SLC22A2 MUTATED SLC22A2 WILD-TYPE
  T0+T1               2                30
  T2                  1                42
  T3                  1                87
  T4                  0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  SLC22A2 MUTATED    2  1  1  0
  SLC22A2 WILD-TYPE 75 68 11  8
D57V5, multiclass
    clus
vv   SLC22A2 MUTATED SLC22A2 WILD-TYPE
  N0               2                75
  N1               1                68
  N2               1                11
  N3               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  SLC22A2 MUTATED     3   1
  SLC22A2 WILD-TYPE 133   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A2 MUTATED      3    1
  SLC22A2 WILD-TYPE  133    8
   clus
vv  SLC22A2 MUTATED SLC22A2 WILD-TYPE
  0               3               133
  1               1                 8
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  SLC22A2 MUTATED     1   3
  SLC22A2 WILD-TYPE  26 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A2 MUTATED      1    3
  SLC22A2 WILD-TYPE   26  155
        clus
vv       SLC22A2 MUTATED SLC22A2 WILD-TYPE
  FEMALE               1                26
  MALE                 3               155
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  SLC22A2 MUTATED     1   2
  SLC22A2 WILD-TYPE 123  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A2 MUTATED      1    2
  SLC22A2 WILD-TYPE  123   41
     clus
vv    SLC22A2 MUTATED SLC22A2 WILD-TYPE
  NO                1               123
  YES               2                41
[1] 2 2
[1] FALSE
D57V9, continuous
[1] "Remove cluster labels:" "SLC22A2 MUTATED"       
clus
  SLC22A2 MUTATED SLC22A2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" "SLC22A2 WILD-TYPE" 
D57V10, binary
                   cls
clus                 0  1
  SLC22A2 MUTATED    3  1
  SLC22A2 WILD-TYPE 86 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A2 MUTATED      3    1
  SLC22A2 WILD-TYPE   86   95
                                   clus
vv                                  SLC22A2 MUTATED SLC22A2 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                   3                86
  ESOPHAGUS SQUAMOUS CELL CARCINOMA               1                95
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  SLC22A2 MUTATED     3   0   0   0
  SLC22A2 WILD-TYPE 134  13   2   7
D57V12, multiclass
    clus
vv   SLC22A2 MUTATED SLC22A2 WILD-TYPE
  R0               3               134
  R1               0                13
  R2               0                 2
  RX               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC22A2 MUTATED       2                         0     2
  SLC22A2 WILD-TYPE    44                         5   112
D57V14, multiclass
                           clus
vv                          SLC22A2 MUTATED SLC22A2 WILD-TYPE
  ASIAN                                   2                44
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   2               112
[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"
D57V15, binary
                   cls
clus                 0  1
  SLC22A2 MUTATED    0  1
  SLC22A2 WILD-TYPE  6 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A2 MUTATED      0    1
  SLC22A2 WILD-TYPE    6   87
                        clus
vv                       SLC22A2 MUTATED SLC22A2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               1                87
[1] 2 2
[1] FALSE

Clustering(58) Variable = PCDH15 MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2               0  1
  PCDH15 MUTATED   12  9
  PCDH15 WILD-TYPE 96 68
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              21              164 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
               9               68 
$`PCDH15 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-IG-A4P3 TCGA-IG-A51D 
       34.85        19.99         5.92         8.94        18.64        17.03 
TCGA-JY-A6FG TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L7-A6VZ 
       41.52        31.56        30.25        32.61         1.38        10.36 
TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-Q9-A6FW TCGA-R6-A6XG TCGA-RE-A7BO 
       13.41        12.46        15.52         7.82        38.40         7.00 
TCGA-VR-A8EX TCGA-XP-A8T8 TCGA-ZR-A9CJ 
       28.11        14.37        19.73 

$`PCDH15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63        13.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN 
        1.32         2.66 

  PCDH15 MUTATED PCDH15 WILD-TYPE 
            1.38             0.13 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
           41.52           122.10 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
          17.030           12.835 
[1] "1.4 - 41.5 (17.0)"  "0.1 - 122.1 (12.8)"
[1] "hr=" "1.1"
D58V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCDH15 MUTATED         2        0        0        0         3         5
  PCDH15 WILD-TYPE       6        5        6        1        44        26
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH15 MUTATED           3          1          1          4        0
  PCDH15 WILD-TYPE        23         13          8          3        5
                  vv
clus               STAGE IVA
  PCDH15 MUTATED           1
  PCDH15 WILD-TYPE         3
D58V3, multiclass
            clus
vv           PCDH15 MUTATED PCDH15 WILD-TYPE
  STAGE I                 2                6
  STAGE IA                0                5
  STAGE IB                0                6
  STAGE II                0                1
  STAGE IIA               3               44
  STAGE IIB               5               26
  STAGE III               3               23
  STAGE IIIA              1               13
  STAGE IIIB              1                8
  STAGE IIIC              4                3
  STAGE IV                0                5
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  PCDH15 MUTATED       6  4 10  0
  PCDH15 WILD-TYPE    26 39 78  5
D58V4, multiclass
       clus
vv      PCDH15 MUTATED PCDH15 WILD-TYPE
  T0+T1              6               26
  T2                 4               39
  T3                10               78
  T4                 0                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PCDH15 MUTATED    6  8  2  4
  PCDH15 WILD-TYPE 71 61 10  4
D58V5, multiclass
    clus
vv   PCDH15 MUTATED PCDH15 WILD-TYPE
  N0              6               71
  N1              8               61
  N2              2               10
  N3              4                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                  cls
clus                 0   1
  PCDH15 MUTATED    15   1
  PCDH15 WILD-TYPE 121   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     15    1
  PCDH15 WILD-TYPE  121    8
   clus
vv  PCDH15 MUTATED PCDH15 WILD-TYPE
  0             15              121
  1              1                8
[1] 2 2
[1] FALSE
D58V7, binary
                  cls
clus                 0   1
  PCDH15 MUTATED     1  20
  PCDH15 WILD-TYPE  26 138
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED      1   20
  PCDH15 WILD-TYPE   26  138
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  FEMALE              1               26
  MALE               20              138
[1] 2 2
[1] FALSE
D58V8, binary
                  cls
clus                 0   1
  PCDH15 MUTATED    16   5
  PCDH15 WILD-TYPE 108  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     16    5
  PCDH15 WILD-TYPE  108   38
     clus
vv    PCDH15 MUTATED PCDH15 WILD-TYPE
  NO              16              108
  YES              5               38
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, binary
                  cls
clus                0  1
  PCDH15 MUTATED   13  8
  PCDH15 WILD-TYPE 76 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     13    8
  PCDH15 WILD-TYPE   76   88
                                   clus
vv                                  PCDH15 MUTATED PCDH15 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 13               76
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              8               88
[1] 2 2
[1] FALSE
D58V11, continuous
                  vv
clus                R0  R1  R2  RX
  PCDH15 MUTATED    17   1   0   2
  PCDH15 WILD-TYPE 120  12   2   5
D58V12, multiclass
    clus
vv   PCDH15 MUTATED PCDH15 WILD-TYPE
  R0             17              120
  R1              1               12
  R2              0                2
  RX              2                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCDH15 MUTATED       3                         1    14
  PCDH15 WILD-TYPE    43                         4   100
D58V14, multiclass
                           clus
vv                          PCDH15 MUTATED PCDH15 WILD-TYPE
  ASIAN                                  3               43
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                 14              100
[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"
D58V15, binary
                  cls
clus                0  1
  PCDH15 MUTATED    1 10
  PCDH15 WILD-TYPE  5 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED      1   10
  PCDH15 WILD-TYPE    5   78
                        clus
vv                       PCDH15 MUTATED PCDH15 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             10               78
[1] 2 2
[1] FALSE

Clustering(59) Variable = KIAA1549 MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  KIAA1549 MUTATED     4   4
  KIAA1549 WILD-TYPE 104  73
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 8                177 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 4                 73 
$`KIAA1549 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3QL TCGA-JY-A6FE TCGA-JY-A93F TCGA-L5-A8NM TCGA-L5-A8NU 
       19.99        35.21         3.68        24.03         7.76        83.24 
TCGA-LN-A7HX TCGA-R6-A6Y2 
       12.23         9.30 

$`KIAA1549 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        5.16        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       13.22         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
              3.68               0.13 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
             83.24             122.10 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
             16.11              13.15 
[1] "3.7 - 83.2 (16.1)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1549 MUTATED         0        0        1        0         3         1
  KIAA1549 WILD-TYPE       8        5        5        1        44        30
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1549 MUTATED           1          0          0          1        0
  KIAA1549 WILD-TYPE        25         14          9          6        5
                    vv
clus                 STAGE IVA
  KIAA1549 MUTATED           0
  KIAA1549 WILD-TYPE         4
D59V3, multiclass
            clus
vv           KIAA1549 MUTATED KIAA1549 WILD-TYPE
  STAGE I                   0                  8
  STAGE IA                  0                  5
  STAGE IB                  1                  5
  STAGE II                  0                  1
  STAGE IIA                 3                 44
  STAGE IIB                 1                 30
  STAGE III                 1                 25
  STAGE IIIA                0                 14
  STAGE IIIB                0                  9
  STAGE IIIC                1                  6
  STAGE IV                  0                  5
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  KIAA1549 MUTATED       0  5  2  0
  KIAA1549 WILD-TYPE    32 38 86  5
D59V4, multiclass
       clus
vv      KIAA1549 MUTATED KIAA1549 WILD-TYPE
  T0+T1                0                 32
  T2                   5                 38
  T3                   2                 86
  T4                   0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  KIAA1549 MUTATED    4  2  0  1
  KIAA1549 WILD-TYPE 73 67 12  7
D59V5, multiclass
    clus
vv   KIAA1549 MUTATED KIAA1549 WILD-TYPE
  N0                4                 73
  N1                2                 67
  N2                0                 12
  N3                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED     6   0
  KIAA1549 WILD-TYPE 130   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      6    0
  KIAA1549 WILD-TYPE  130    9
   clus
vv  KIAA1549 MUTATED KIAA1549 WILD-TYPE
  0                6                130
  1                0                  9
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED     2   6
  KIAA1549 WILD-TYPE  25 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      2    6
  KIAA1549 WILD-TYPE   25  152
        clus
vv       KIAA1549 MUTATED KIAA1549 WILD-TYPE
  FEMALE                2                 25
  MALE                  6                152
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED     6   1
  KIAA1549 WILD-TYPE 118  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      6    1
  KIAA1549 WILD-TYPE  118   42
     clus
vv    KIAA1549 MUTATED KIAA1549 WILD-TYPE
  NO                 6                118
  YES                1                 42
[1] 2 2
[1] FALSE
D59V9, continuous
[1] "Remove cluster labels:" "KIAA1549 MUTATED"      
clus
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A51D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A7DP         TCGA-KH-A6WC 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-A7RE 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-V5-AASW         TCGA-V5-AASX 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
D59V10, binary
                    cls
clus                  0  1
  KIAA1549 MUTATED    4  4
  KIAA1549 WILD-TYPE 85 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      4    4
  KIAA1549 WILD-TYPE   85   92
                                   clus
vv                                  KIAA1549 MUTATED KIAA1549 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                    4                 85
  ESOPHAGUS SQUAMOUS CELL CARCINOMA                4                 92
[1] 2 2
[1] FALSE
D59V11, continuous
                    vv
clus                  R0  R1  R2  RX
  KIAA1549 MUTATED     7   0   0   0
  KIAA1549 WILD-TYPE 130  13   2   7
D59V12, multiclass
    clus
vv   KIAA1549 MUTATED KIAA1549 WILD-TYPE
  R0                7                130
  R1                0                 13
  R2                0                  2
  RX                0                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1549 MUTATED       1                         0     7
  KIAA1549 WILD-TYPE    45                         5   107
D59V14, multiclass
                           clus
vv                          KIAA1549 MUTATED KIAA1549 WILD-TYPE
  ASIAN                                    1                 45
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    7                107
[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"
D59V15, binary
                    cls
clus                  0  1
  KIAA1549 MUTATED    1  2
  KIAA1549 WILD-TYPE  5 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      1    2
  KIAA1549 WILD-TYPE    5   86
                        clus
vv                       KIAA1549 MUTATED KIAA1549 WILD-TYPE
  HISPANIC OR LATINO                    1                  5
  NOT HISPANIC OR LATINO                2                 86
[1] 2 2
[1] FALSE

Clustering(60) Variable = SETBP1 MUTATION ANALYSIS
D60V1, survival
                  sevent
clus2                0   1
  SETBP1 MUTATED     5   9
  SETBP1 WILD-TYPE 103  68
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              14              171 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
               9               68 
$`SETBP1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NG TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-KH-A6WC 
       60.39        35.97         5.92         0.85        18.64         6.28 
TCGA-L5-A4OT TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-R6-A8WG 
        4.90        16.47         7.76        21.37        52.57        12.69 
TCGA-RE-A7BO TCGA-V5-A7RE 
        7.00        16.44 

$`SETBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27        35.21        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.55        13.22         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.89         2.30        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        1.32         2.66        19.73 

  SETBP1 MUTATED SETBP1 WILD-TYPE 
            0.85             0.13 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
           60.39           122.10 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
          14.565           13.150 
[1] "0.8 - 60.4 (14.6)"  "0.1 - 122.1 (13.2)"
[1] "hr=" "1.4"
D60V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETBP1 MUTATED         1        1        1        0         2         3
  SETBP1 WILD-TYPE       7        4        5        1        45        28
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SETBP1 MUTATED           3          1          0          0        1
  SETBP1 WILD-TYPE        23         13          9          7        4
                  vv
clus               STAGE IVA
  SETBP1 MUTATED           0
  SETBP1 WILD-TYPE         4
D60V3, multiclass
            clus
vv           SETBP1 MUTATED SETBP1 WILD-TYPE
  STAGE I                 1                7
  STAGE IA                1                4
  STAGE IB                1                5
  STAGE II                0                1
  STAGE IIA               2               45
  STAGE IIB               3               28
  STAGE III               3               23
  STAGE IIIA              1               13
  STAGE IIIB              0                9
  STAGE IIIC              0                7
  STAGE IV                1                4
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1 T2 T3 T4
  SETBP1 MUTATED       4  3  5  1
  SETBP1 WILD-TYPE    28 40 83  4
D60V4, multiclass
       clus
vv      SETBP1 MUTATED SETBP1 WILD-TYPE
  T0+T1              4               28
  T2                 3               40
  T3                 5               83
  T4                 1                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  SETBP1 MUTATED    6  7  0  0
  SETBP1 WILD-TYPE 71 62 12  8
D60V5, multiclass
    clus
vv   SETBP1 MUTATED SETBP1 WILD-TYPE
  N0              6               71
  N1              7               62
  N2              0               12
  N3              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                  cls
clus                 0   1
  SETBP1 MUTATED    12   1
  SETBP1 WILD-TYPE 124   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     12    1
  SETBP1 WILD-TYPE  124    8
   clus
vv  SETBP1 MUTATED SETBP1 WILD-TYPE
  0             12              124
  1              1                8
[1] 2 2
[1] FALSE
D60V7, binary
                  cls
clus                 0   1
  SETBP1 MUTATED     2  12
  SETBP1 WILD-TYPE  25 146
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED      2   12
  SETBP1 WILD-TYPE   25  146
        clus
vv       SETBP1 MUTATED SETBP1 WILD-TYPE
  FEMALE              2               25
  MALE               12              146
[1] 2 2
[1] FALSE
D60V8, binary
                  cls
clus                 0   1
  SETBP1 MUTATED    11   3
  SETBP1 WILD-TYPE 113  40
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     11    3
  SETBP1 WILD-TYPE  113   40
     clus
vv    SETBP1 MUTATED SETBP1 WILD-TYPE
  NO              11              113
  YES              3               40
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, binary
                  cls
clus                0  1
  SETBP1 MUTATED   10  4
  SETBP1 WILD-TYPE 79 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     10    4
  SETBP1 WILD-TYPE   79   92
                                   clus
vv                                  SETBP1 MUTATED SETBP1 WILD-TYPE
  ESOPHAGUS ADENOCARCINOMA, NOS                 10               79
  ESOPHAGUS SQUAMOUS CELL CARCINOMA              4               92
[1] 2 2
[1] FALSE
D60V11, continuous
                  vv
clus                R0  R1  R2  RX
  SETBP1 MUTATED    10   2   0   0
  SETBP1 WILD-TYPE 127  11   2   7
D60V12, multiclass
    clus
vv   SETBP1 MUTATED SETBP1 WILD-TYPE
  R0             10              127
  R1              2               11
  R2              0                2
  RX              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETBP1 MUTATED       0                         0    13
  SETBP1 WILD-TYPE    46                         5   101
D60V14, multiclass
                           clus
vv                          SETBP1 MUTATED SETBP1 WILD-TYPE
  ASIAN                                  0               46
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 13              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                  cls
clus                0  1
  SETBP1 MUTATED    1  5
  SETBP1 WILD-TYPE  5 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED      1    5
  SETBP1 WILD-TYPE    5   83
                        clus
vv                       SETBP1 MUTATED SETBP1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              5               83
[1] 2 2
[1] FALSE
