[1] "ofn"        "-oTTGCT-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/TGCT-TP/22507091/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/22569791/transformed.cor.cli.txt"

nPatients in clinical file=134, in cluster file=147, common to both=131
[1] "Reduce the number of clustering variables from 61 to 54."
[1]  54 131
[1] "FAM18B2 MUTATION ANALYSIS"
[1] 3
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               21               110 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               21               110 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
           25           106 
  KIT MUTATED KIT WILD-TYPE 
           25           106 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            19            112 
  KRAS MUTATED KRAS WILD-TYPE 
            19            112 
[1] "FAM104B MUTATION ANALYSIS"
[1] 3
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               125 
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               125 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             6            125 
  NRAS MUTATED NRAS WILD-TYPE 
             6            125 
[1] "DDX11 MUTATION ANALYSIS"
[1] 3
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             125 
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             125 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            118 
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            118 
[1] "PNPLA4 MUTATION ANALYSIS"
[1] 3
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              126 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              126 
[1] "SERINC2 MUTATION ANALYSIS"
[1] 3
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               128 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               128 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             125 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             125 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             127 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             127 
[1] "HSF4 MUTATION ANALYSIS"
[1] 3
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            125 
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            125 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             125 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             125 
[1] "MLLT3 MUTATION ANALYSIS"
[1] 3
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             128 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             128 
[1] "ERC1 MUTATION ANALYSIS"
[1] 3
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            125 
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            125 
[1] "SP8 MUTATION ANALYSIS"
[1] 3
  SP8 MUTATED SP8 WILD-TYPE 
            4           127 
  SP8 MUTATED SP8 WILD-TYPE 
            4           127 
[1] "NAT10 MUTATION ANALYSIS"
[1] 3
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             127 
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             127 
[1] "SPIN2A MUTATION ANALYSIS"
[1] 3
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              128 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              128 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            5           126 
  DEK MUTATED DEK WILD-TYPE 
            5           126 
[1] "FANK1 MUTATION ANALYSIS"
[1] 3
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             127 
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             127 
[1] "ANKRD11 MUTATION ANALYSIS"
[1] 3
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               126 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               126 
[1] "ATXN3 MUTATION ANALYSIS"
[1] 3
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             128 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             128 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             127 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             127 
[1] "KRTAP10-10 MUTATION ANALYSIS"
[1] 3
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  127 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  127 
[1] "ZNF680 MUTATION ANALYSIS"
[1] 3
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               3              128 
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               3              128 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            127 
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            127 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               7              124 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               7              124 
[1] "FAM8A1 MUTATION ANALYSIS"
[1] 3
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              128 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              128 
[1] "PSMD11 MUTATION ANALYSIS"
[1] 3
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              127 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              127 
[1] "KRTAP1-1 MUTATION ANALYSIS"
[1] 3
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                128 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                128 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             127 
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             127 
[1] "FAM101B MUTATION ANALYSIS"
[1] 3
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               127 
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               127 
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            117 
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            117 
[1] "HTT MUTATION ANALYSIS"
[1] 3
  HTT MUTATED HTT WILD-TYPE 
            3           128 
  HTT MUTATED HTT WILD-TYPE 
            3           128 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            127 
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            127 
[1] "PABPC3 MUTATION ANALYSIS"
[1] 3
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              128 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              128 
[1] "CUX1 MUTATION ANALYSIS"
[1] 3
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            126 
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            126 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            128 
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            128 
[1] "STAB1 MUTATION ANALYSIS"
[1] 3
  STAB1 MUTATED STAB1 WILD-TYPE 
              7             124 
  STAB1 MUTATED STAB1 WILD-TYPE 
              7             124 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               5              126 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               5              126 
[1] "AHDC1 MUTATION ANALYSIS"
[1] 3
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             128 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             128 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             127 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             127 
[1] "PIK3CD MUTATION ANALYSIS"
[1] 3
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              128 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              128 
[1] "BCL11B MUTATION ANALYSIS"
[1] 3
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              126 
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              126 
[1] "KIAA0430 MUTATION ANALYSIS"
[1] 3
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 3                128 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 3                128 
[1] "MTIF3 MUTATION ANALYSIS"
[1] 3
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             128 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             128 
[1] "BTN2A2 MUTATION ANALYSIS"
[1] 3
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              128 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              128 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             127 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             127 
[1] "SSBP3 MUTATION ANALYSIS"
[1] 3
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             128 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             128 
[1] "SP4 MUTATION ANALYSIS"
[1] 3
  SP4 MUTATED SP4 WILD-TYPE 
            3           128 
  SP4 MUTATED SP4 WILD-TYPE 
            3           128 
[1] "PCMTD1 MUTATION ANALYSIS"
[1] 3
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              126 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              126 
[1] "RBM3 MUTATION ANALYSIS"
[1] 3
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            128 
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            128 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               4              127 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               4              127 
[1] "TTC38 MUTATION ANALYSIS"
[1] 3
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             127 
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             127 
[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] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 131 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=4,	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=127,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	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=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 131 columns, 1 survival variables, and 9 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"           "RADIATION_THERAPY"          
[7] "KARNOFSKY_PERFORMANCE_SCORE" "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
74 50  6 
[1] "table(vv)"
vv
T1 T2 T3 
74 50  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
74 50  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
74 50  6 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
45 10  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   45    12 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
45 10  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 45

$Class1_nSamples
[1] 12

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   45    12 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=3, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = FAM18B2 MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  FAM18B2 MUTATED    21   0
  FAM18B2 WILD-TYPE 106   4
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               21               110 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                0                 4 
$`FAM18B2 MUTATED`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFL TCGA-2G-AAG8 
       50.27        52.37        76.11       128.58        24.66        75.25 
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGN TCGA-2G-AAGV TCGA-2G-AAHC TCGA-2G-AAHT 
       84.99        89.88       120.20       148.83       182.10        17.82 
TCGA-2G-AALP TCGA-S6-A8JY TCGA-SN-A84W TCGA-SO-A8JP TCGA-XE-A8H4 TCGA-XE-AAO3 
       86.96         9.14         9.63        17.75        18.38        93.93 
TCGA-XY-A89B TCGA-YU-A90W TCGA-YU-A94I 
       15.48        36.59        17.62 

$`FAM18B2 WILD-TYPE`
TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAFG 
       26.66        20.32        41.39        46.13       114.77       203.28 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       45.21        22.19        26.04        16.54        25.41        22.52 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 
       45.67        36.13        44.48        75.58        73.35        81.37 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       73.45        80.19        81.47        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      119.05       127.92       132.36       132.10       158.33       144.85 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      161.06       181.28       175.20       172.04       180.07       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       204.16        73.91       110.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      211.89       186.31       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      229.22       244.50       131.21        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
       17.03         0.10        15.88        22.95        18.15        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA 
        1.38        16.31        10.26        17.23        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
       50.96         0.43        22.09        27.72         9.24        68.02 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L 
       64.57        31.92         0.56        28.47        71.24        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
             9.14              0.10 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
            182.1             244.5 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
            52.37             40.70 
[1] "9.1 - 182.1 (52.4)" "0.1 - 244.5 (40.7)"
[1] "hr="     "8.6e+07"
D1V2, continuous
                   vv
clus                IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM18B2 MUTATED    8       3        5        2        0         0         0
  FAM18B2 WILD-TYPE 38      15       20        9        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM18B2 MUTATED           0         0          0          2          0
  FAM18B2 WILD-TYPE         1         2          1          4          5
D1V3, multiclass
            clus
vv           FAM18B2 MUTATED FAM18B2 WILD-TYPE
  IS                       8                38
  STAGE I                  3                15
  STAGE IA                 5                20
  STAGE IB                 2                 9
  STAGE II                 0                 4
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               2                 4
  STAGE IIIC               0                 5
[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                T1 T2 T3
  FAM18B2 MUTATED   11  9  0
  FAM18B2 WILD-TYPE 63 41  6
D1V4, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  T1              11                63
  T2               9                41
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  FAM18B2 MUTATED    9     1
  FAM18B2 WILD-TYPE 36    11
D1V5, multiclass
       clus
vv      FAM18B2 MUTATED FAM18B2 WILD-TYPE
  N0                  9                36
  N1+N2               1                11
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED   18  1
  FAM18B2 WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     18    1
  FAM18B2 WILD-TYPE   95    3
   clus
vv  FAM18B2 MUTATED FAM18B2 WILD-TYPE
  0              18                95
  1               1                 3
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED   16  5
  FAM18B2 WILD-TYPE 92 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     16    5
  FAM18B2 WILD-TYPE   92   16
     clus
vv    FAM18B2 MUTATED FAM18B2 WILD-TYPE
  NO               16                92
  YES               5                16
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM18B2 MUTATED       1                         0    19
  FAM18B2 WILD-TYPE     3                         6    97
D1V9, multiclass
                           clus
vv                          FAM18B2 MUTATED FAM18B2 WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  19                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"
D1V10, binary
                   cls
clus                 0  1
  FAM18B2 MUTATED    1 18
  FAM18B2 WILD-TYPE 11 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1   18
  FAM18B2 WILD-TYPE   11   91
                        clus
vv                       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO              18                91
[1] 2 2
[1] FALSE

Clustering(2) Variable = KIT MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  KIT MUTATED    25   0
  KIT WILD-TYPE 102   4
  KIT MUTATED KIT WILD-TYPE 
           25           106 
  KIT MUTATED KIT WILD-TYPE 
            0             4 
$`KIT MUTATED`
TCGA-ZM-AA0E TCGA-2G-AAF1 TCGA-2G-AAG9 TCGA-2G-AAGI TCGA-2G-AAH3 TCGA-2G-AAHA 
       26.66        46.13        73.45       103.13        59.90       110.10 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      232.80       211.89        17.82        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-VF-A8AA TCGA-WZ-A7V5 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOF 
       17.03        37.68        34.88         0.46        55.92        41.69 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0F 
       64.57        31.92        28.47        37.02        27.88        22.39 
TCGA-ZM-AA0H 
       57.07 

$`KIT WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 
       50.27        52.37        20.32        41.39        76.11       114.77 
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      128.58       203.28        45.21        22.19        26.04        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        25.41        22.52        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC 
       75.58        73.35        81.37        75.25        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       81.47        89.88        85.84        96.59       119.05       127.92 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      120.20       132.36       132.10       158.33       144.85       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      161.06       181.28       175.20       172.04       180.07       199.23 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD 
      204.16        73.91       182.10        59.80       186.31       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       86.96         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       17.75        37.18        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52        24.26        24.76        29.39        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       68.02        36.59         0.56        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       28.41        49.25        27.55        20.84 

  KIT MUTATED KIT WILD-TYPE 
         0.46          0.10 
  KIT MUTATED KIT WILD-TYPE 
        232.8         244.5 
  KIT MUTATED KIT WILD-TYPE 
       37.020        44.845 
[1] "0.5 - 232.8 (37.0)" "0.1 - 244.5 (44.8)"
[1] "hr="     "2.6e+08"
D2V2, continuous
               vv
clus            IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIT MUTATED    5       8        6        3        0         0         0
  KIT WILD-TYPE 41      10       19        8        4         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KIT MUTATED           1         0          0          1          1
  KIT WILD-TYPE         0         2          1          5          4
D2V3, multiclass
            clus
vv           KIT MUTATED KIT WILD-TYPE
  IS                   5            41
  STAGE I              8            10
  STAGE IA             6            19
  STAGE IB             3             8
  STAGE II             0             4
  STAGE IIA            0             5
  STAGE IIB            0             1
  STAGE IIC            1             0
  STAGE III            0             2
  STAGE IIIA           0             1
  STAGE IIIB           1             5
  STAGE IIIC           1             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            T1 T2 T3
  KIT MUTATED   12 12  1
  KIT WILD-TYPE 62 38  5
D2V4, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  T1          12            62
  T2          12            38
  T3           1             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  KIT MUTATED    8     1
  KIT WILD-TYPE 37    11
D2V5, multiclass
       clus
vv      KIT MUTATED KIT WILD-TYPE
  N0              8            37
  N1+N2           1            11
[1] 2 2
[1] FALSE
D2V6, binary
               cls
clus             0  1
  KIT MUTATED   21  0
  KIT WILD-TYPE 92  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     21    0
  KIT WILD-TYPE   92    4
   clus
vv  KIT MUTATED KIT WILD-TYPE
  0          21            92
  1           0             4
[1] 2 2
[1] FALSE
D2V7, binary
               cls
clus             0  1
  KIT MUTATED   17  7
  KIT WILD-TYPE 91 14
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     17    7
  KIT WILD-TYPE   91   14
     clus
vv    KIT MUTATED KIT WILD-TYPE
  NO           17            91
  YES           7            14
[1] 2 2
[1] FALSE
D2V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED       2                         1    20
  KIT WILD-TYPE     2                         5    96
D2V9, multiclass
                           clus
vv                          KIT MUTATED KIT WILD-TYPE
  ASIAN                               2             2
  BLACK OR AFRICAN AMERICAN           1             5
  WHITE                              20            96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
               cls
clus             0  1
  KIT MUTATED    1 21
  KIT WILD-TYPE 11 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      1   21
  KIT WILD-TYPE   11   88
                        clus
vv                       KIT MUTATED KIT WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO          21            88
[1] 2 2
[1] FALSE

Clustering(3) Variable = KRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    18   1
  KRAS WILD-TYPE 109   3
  KRAS MUTATED KRAS WILD-TYPE 
            19            112 
  KRAS MUTATED KRAS WILD-TYPE 
             1              3 
$`KRAS MUTATED`
TCGA-2G-AAG3 TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAG9 TCGA-2G-AAH8 
       52.37        20.32        76.11       114.77        73.45        73.91 
TCGA-2G-AAHA TCGA-2G-AAHP TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A76C 
      110.10       186.31        17.03        15.88        22.95         1.38 
TCGA-VF-A8AC TCGA-W4-A7U2 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XY-A9T9 
       35.61        41.52        25.45        18.38        40.01         9.24 
TCGA-ZM-AA05 
       37.02 

$`KRAS WILD-TYPE`
TCGA-2G-AAG0 TCGA-ZM-AA0E TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFG 
       50.27        26.66        41.39        46.13       128.58       203.28 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       45.21        22.19        26.04        24.66        16.54        25.41 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       22.52        45.67        36.13        44.48        75.58        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       81.37        75.25        80.19        84.99        81.47        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       85.84       103.13        96.59       119.05       127.92       120.20 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      132.36       132.10       158.33       144.85       148.83       161.06 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      181.28       175.20       172.04       180.07       199.23        59.90 
TCGA-2G-AAH4 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT 
      204.16       182.10        59.80       232.80       211.89        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
      131.21        86.96        14.30        19.96        14.33         0.10 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
       18.15         9.14        13.58        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD 
       17.23        17.75        37.18        37.68        24.99        33.07 
TCGA-VF-A8AE TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
       23.90        24.26        24.76        29.39        34.88        28.14 
TCGA-XE-A8H1 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        6.87        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       68.02        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       71.24        17.62        51.72        28.41        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        22.39        57.07        20.84 

  KRAS MUTATED KRAS WILD-TYPE 
          1.38           0.10 
  KRAS MUTATED KRAS WILD-TYPE 
        186.31         244.50 
  KRAS MUTATED KRAS WILD-TYPE 
        37.020         44.845 
[1] "1.4 - 186.3 (37.0)" "0.1 - 244.5 (44.8)"
[1] "hr=" "3"  
D3V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED    8       1        3        1        0         0         0
  KRAS WILD-TYPE 38      17       22       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRAS MUTATED           1         0          0          1          1
  KRAS WILD-TYPE         0         2          1          5          4
D3V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  IS                    8             38
  STAGE I               1             17
  STAGE IA              3             22
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             1              0
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            1              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             T1 T2 T3
  KRAS MUTATED    9  8  1
  KRAS WILD-TYPE 65 42  5
D3V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            9             65
  T2            8             42
  T3            1              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  KRAS MUTATED    6     1
  KRAS WILD-TYPE 39    11
D3V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0               6             39
  N1+N2            1             11
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus              0  1
  KRAS MUTATED   18  0
  KRAS WILD-TYPE 95  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     18    0
  KRAS WILD-TYPE   95    4
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           18             95
  1            0              4
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus              0  1
  KRAS MUTATED   12  7
  KRAS WILD-TYPE 96 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     12    7
  KRAS WILD-TYPE   96   14
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            12             96
  YES            7             14
[1] 2 2
[1] FALSE
D3V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0    18
  KRAS WILD-TYPE     4                         6    98
D3V9, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               18             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                cls
clus              0  1
  KRAS MUTATED    1 18
  KRAS WILD-TYPE 11 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1   18
  KRAS WILD-TYPE   11   91
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO           18             91
[1] 2 2
[1] FALSE

Clustering(4) Variable = FAM104B MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  FAM104B MUTATED     6   0
  FAM104B WILD-TYPE 121   4
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               125 
  FAM104B MUTATED FAM104B WILD-TYPE 
                0                 4 
$`FAM104B MUTATED`
TCGA-2G-AAKL TCGA-2X-A9D5 TCGA-SB-A76C TCGA-WZ-A7V4 TCGA-XE-AAO4 TCGA-YU-A90Q 
      230.89        14.30         1.38        29.39        12.07        64.57 

$`FAM104B WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM 
      186.31        17.82       208.44       216.92       225.60       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      244.50       131.21        86.96        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.26        24.76        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       55.92        93.93         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        9.24        68.02        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  FAM104B MUTATED FAM104B WILD-TYPE 
             1.38              0.10 
  FAM104B MUTATED FAM104B WILD-TYPE 
           230.89            244.50 
  FAM104B MUTATED FAM104B WILD-TYPE 
           21.845            41.690 
[1] "1.4 - 230.9 (21.8)" "0.1 - 244.5 (41.7)"
[1] "hr="     "9.3e+07"
D4V2, continuous
                   vv
clus                IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM104B MUTATED    0       2        1        1        1         0         0
  FAM104B WILD-TYPE 46      16       24       10        3         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM104B MUTATED           0         0          0          0          0
  FAM104B WILD-TYPE         1         2          1          6          5
D4V3, multiclass
            clus
vv           FAM104B MUTATED FAM104B WILD-TYPE
  IS                       0                46
  STAGE I                  2                16
  STAGE IA                 1                24
  STAGE IB                 1                10
  STAGE II                 1                 3
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
[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                T1 T2 T3
  FAM104B MUTATED    4  2  0
  FAM104B WILD-TYPE 70 48  6
D4V4, multiclass
    clus
vv   FAM104B MUTATED FAM104B WILD-TYPE
  T1               4                70
  T2               2                48
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  FAM104B MUTATED    0     0
  FAM104B WILD-TYPE 45    12
D4V5, multiclass
D4V6, binary
                   cls
clus                  0   1
  FAM104B MUTATED     4   0
  FAM104B WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104B MUTATED      4    0
  FAM104B WILD-TYPE  109    4
   clus
vv  FAM104B MUTATED FAM104B WILD-TYPE
  0               4               109
  1               0                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  FAM104B MUTATED     6   0
  FAM104B WILD-TYPE 102  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104B MUTATED      6    0
  FAM104B WILD-TYPE  102   21
     clus
vv    FAM104B MUTATED FAM104B WILD-TYPE
  NO                6               102
  YES               0                21
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM104B MUTATED       0                         0     5
  FAM104B WILD-TYPE     4                         6   111
D4V9, multiclass
                           clus
vv                          FAM104B MUTATED FAM104B WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5               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"
D4V10, binary
                   cls
clus                  0   1
  FAM104B MUTATED     1   4
  FAM104B WILD-TYPE  11 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104B MUTATED      1    4
  FAM104B WILD-TYPE   11  105
                        clus
vv                       FAM104B MUTATED FAM104B WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4               105
[1] 2 2
[1] FALSE

Clustering(5) Variable = NRAS MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     6   0
  NRAS WILD-TYPE 121   4
  NRAS MUTATED NRAS WILD-TYPE 
             6            125 
  NRAS MUTATED NRAS WILD-TYPE 
             0              4 
$`NRAS MUTATED`
TCGA-SB-A76C TCGA-WZ-A7V4 TCGA-XE-AAO6 TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90Q 
        1.38        29.39         7.89        41.69        15.48        64.57 

$`NRAS WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      186.31        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       244.50       131.21        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.33        17.03         0.10        15.88        22.95        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
        9.14        13.58        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.75        37.18        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       23.90        41.52        24.26        24.76        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       65.98         0.46        55.92        93.93        12.07        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 
        8.88        67.66        50.96         0.43        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        9.24        68.02        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  NRAS MUTATED NRAS WILD-TYPE 
          1.38           0.10 
  NRAS MUTATED NRAS WILD-TYPE 
         64.57         244.50 
  NRAS MUTATED NRAS WILD-TYPE 
        22.435         44.480 
[1] "1.4 - 64.6 (22.4)"  "0.1 - 244.5 (44.5)"
[1] "hr="     "2.6e+07"
D5V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRAS MUTATED    0       1        3        1        0         0         0
  NRAS WILD-TYPE 46      17       22       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NRAS MUTATED           0         0          0          0          0
  NRAS WILD-TYPE         1         2          1          6          5
D5V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  IS                    0             46
  STAGE I               1             17
  STAGE IA              3             22
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  NRAS MUTATED    5  1  0
  NRAS WILD-TYPE 69 49  6
D5V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            5             69
  T2            1             49
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  NRAS MUTATED    0     0
  NRAS WILD-TYPE 45    12
D5V5, multiclass
D5V6, binary
                cls
clus               0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 109   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    0
  NRAS WILD-TYPE  109    4
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            4            109
  1            0              4
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  NRAS MUTATED     4   2
  NRAS WILD-TYPE 104  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    2
  NRAS WILD-TYPE  104   19
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             4            104
  YES            2             19
[1] 2 2
[1] FALSE
D5V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       1                         0     4
  NRAS WILD-TYPE     3                         6   112
D5V9, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D5V10, binary
                cls
clus               0   1
  NRAS MUTATED     0   5
  NRAS WILD-TYPE  12 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    5
  NRAS WILD-TYPE   12  104
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(6) Variable = DDX11 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  DDX11 MUTATED     6   0
  DDX11 WILD-TYPE 121   4
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             125 
  DDX11 MUTATED DDX11 WILD-TYPE 
              0               4 
$`DDX11 MUTATED`
TCGA-2G-AAFY TCGA-2G-AAGC TCGA-2G-AAKH TCGA-S6-A8JY TCGA-WZ-A7V3 TCGA-YU-A912 
       36.13        84.99       225.60         9.14        24.76        28.47 

$`DDX11 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       80.19        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      208.44       216.92       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       15.88        22.95        18.15        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  DDX11 MUTATED DDX11 WILD-TYPE 
           9.14            0.10 
  DDX11 MUTATED DDX11 WILD-TYPE 
          225.6           244.5 
  DDX11 MUTATED DDX11 WILD-TYPE 
          32.30           41.69 
[1] "9.1 - 225.6 (32.3)" "0.1 - 244.5 (41.7)"
[1] "hr="     "2.6e+07"
D6V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX11 MUTATED    2       1        0        0        1         1         0
  DDX11 WILD-TYPE 44      17       25       11        3         4         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DDX11 MUTATED           0         0          0          0          1
  DDX11 WILD-TYPE         1         2          1          6          4
D6V3, multiclass
            clus
vv           DDX11 MUTATED DDX11 WILD-TYPE
  IS                     2              44
  STAGE I                1              17
  STAGE IA               0              25
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              1               4
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             1               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              T1 T2 T3
  DDX11 MUTATED    5  1  0
  DDX11 WILD-TYPE 69 49  6
D6V4, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  T1             5              69
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  DDX11 MUTATED    1     1
  DDX11 WILD-TYPE 44    11
D6V5, multiclass
[1] "Remove cluster labels:" "DDX11 MUTATED"         
clus
  DDX11 MUTATED DDX11 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGE      TCGA-2G-AAGF 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGW      TCGA-2G-AAGX      TCGA-2G-AAGY 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG      TCGA-2G-AAHL 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKG 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G      TCGA-4K-AA1H 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP      TCGA-VF-A8A8 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
D6V6, binary
                 cls
clus                0   1
  DDX11 MUTATED     4   0
  DDX11 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      4    0
  DDX11 WILD-TYPE  109    4
   clus
vv  DDX11 MUTATED DDX11 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  DDX11 MUTATED     6   0
  DDX11 WILD-TYPE 102  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      6    0
  DDX11 WILD-TYPE  102   21
     clus
vv    DDX11 MUTATED DDX11 WILD-TYPE
  NO              6             102
  YES             0              21
[1] 2 2
[1] FALSE
D6V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX11 MUTATED       0                         1     5
  DDX11 WILD-TYPE     4                         5   111
D6V9, multiclass
                           clus
vv                          DDX11 MUTATED DDX11 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 5             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"
D6V10, binary
                 cls
clus                0   1
  DDX11 MUTATED     0   5
  DDX11 WILD-TYPE  12 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      0    5
  DDX11 WILD-TYPE   12  104
                        clus
vv                       DDX11 MUTATED DDX11 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             5             104
[1] 2 2
[1] FALSE

Clustering(7) Variable = MUC6 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  MUC6 MUTATED    13   0
  MUC6 WILD-TYPE 114   4
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            118 
  MUC6 MUTATED MUC6 WILD-TYPE 
             0              4 
$`MUC6 MUTATED`
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAGN TCGA-2G-AAGW TCGA-2G-AAHC 
       52.37        26.04        22.52       120.20       161.06       182.10 
TCGA-2G-AAHN TCGA-2G-AAKG TCGA-S6-A8JW TCGA-W4-A7U4 TCGA-XE-A8H4 TCGA-XE-A8H5 
      211.89       216.92        22.95        24.26        18.38        40.01 
TCGA-XY-A9T9 
        9.24 

$`MUC6 WILD-TYPE`
TCGA-2G-AAG0 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
      114.77       128.58       203.28        45.21        22.19        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 
       16.54        25.41        45.67        36.13        44.48        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84       103.13        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      127.92       132.36       132.10       158.33       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 
      181.28       175.20       172.04       180.07       199.23        59.90 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP 
      204.16        73.91       110.10        59.80       232.80       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        15.88        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       23.28        34.22        65.98         0.46        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       50.96         0.43        15.48        22.09        27.72        68.02 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       64.57        31.92        36.59         0.56        28.47        71.24 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       17.62        51.72        28.41        37.02        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        22.39        57.07        20.84 

  MUC6 MUTATED MUC6 WILD-TYPE 
          9.24           0.10 
  MUC6 MUTATED MUC6 WILD-TYPE 
        216.92         244.50 
  MUC6 MUTATED MUC6 WILD-TYPE 
        40.010         41.605 
[1] "9.2 - 216.9 (40.0)" "0.1 - 244.5 (41.6)"
[1] "hr="     "7.9e+07"
D7V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC6 MUTATED    6       2        1        0        0         1         0
  MUC6 WILD-TYPE 40      16       24       11        4         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC6 MUTATED           0         0          0          1          0
  MUC6 WILD-TYPE         1         2          1          5          5
D7V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  IS                    6             40
  STAGE I               2             16
  STAGE IA              1             24
  STAGE IB              0             11
  STAGE II              0              4
  STAGE IIA             1              4
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            0              5
[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             T1 T2 T3
  MUC6 MUTATED    9  3  0
  MUC6 WILD-TYPE 65 47  6
D7V4, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  T1            9             65
  T2            3             47
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  MUC6 MUTATED    4     2
  MUC6 WILD-TYPE 41    10
D7V5, multiclass
       clus
vv      MUC6 MUTATED MUC6 WILD-TYPE
  N0               4             41
  N1+N2            2             10
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus               0   1
  MUC6 MUTATED    13   0
  MUC6 WILD-TYPE 100   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     13    0
  MUC6 WILD-TYPE  100    4
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           13            100
  1            0              4
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus              0  1
  MUC6 MUTATED    9  4
  MUC6 WILD-TYPE 99 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      9    4
  MUC6 WILD-TYPE   99   17
     clus
vv    MUC6 MUTATED MUC6 WILD-TYPE
  NO             9             99
  YES            4             17
[1] 2 2
[1] FALSE
D7V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC6 MUTATED       1                         0    11
  MUC6 WILD-TYPE     3                         6   105
D7V9, multiclass
                           clus
vv                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               11            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"
D7V10, binary
                cls
clus              0  1
  MUC6 MUTATED    1 12
  MUC6 WILD-TYPE 11 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      1   12
  MUC6 WILD-TYPE   11   97
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO           12             97
[1] 2 2
[1] FALSE

Clustering(8) Variable = PNPLA4 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  PNPLA4 MUTATED     5   0
  PNPLA4 WILD-TYPE 122   4
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              126 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               0                4 
$`PNPLA4 MUTATED`
TCGA-2G-AAFY TCGA-2G-AAGK TCGA-2G-AAHA TCGA-XE-AAO4 TCGA-YU-A90Q 
       36.13       119.05       110.10        12.07        64.57 

$`PNPLA4 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       96.59       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC 
      180.07       199.23        59.90       204.16        73.91       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
        0.46        55.92        93.93         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       27.72         9.24        68.02        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
           12.07             0.10 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
          119.05           244.50 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
          64.570           41.455 
[1] "12.1 - 119.0 (64.6)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "2.6e+07"
D8V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNPLA4 MUTATED    1       0        1        2        0         1         0
  PNPLA4 WILD-TYPE 45      18       24        9        4         4         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PNPLA4 MUTATED           0         0          0          0          0
  PNPLA4 WILD-TYPE         1         2          1          6          5
D8V3, multiclass
            clus
vv           PNPLA4 MUTATED PNPLA4 WILD-TYPE
  IS                      1               45
  STAGE I                 0               18
  STAGE IA                1               24
  STAGE IB                2                9
  STAGE II                0                4
  STAGE IIA               1                4
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  PNPLA4 MUTATED    1  4  0
  PNPLA4 WILD-TYPE 73 46  6
D8V4, multiclass
    clus
vv   PNPLA4 MUTATED PNPLA4 WILD-TYPE
  T1              1               73
  T2              4               46
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PNPLA4 MUTATED    1     1
  PNPLA4 WILD-TYPE 44    11
D8V5, multiclass
[1] "Remove cluster labels:" "PNPLA4 MUTATED"        
clus
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               2               55 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX       TCGA-2G-AAGY 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG       TCGA-2G-AAHL 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKG 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G       TCGA-4K-AA1H 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP       TCGA-VF-A8A8 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
D8V6, binary
                  cls
clus                 0   1
  PNPLA4 MUTATED     4   0
  PNPLA4 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA4 MUTATED      4    0
  PNPLA4 WILD-TYPE  109    4
   clus
vv  PNPLA4 MUTATED PNPLA4 WILD-TYPE
  0              4              109
  1              0                4
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  PNPLA4 MUTATED     5   0
  PNPLA4 WILD-TYPE 103  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA4 MUTATED      5    0
  PNPLA4 WILD-TYPE  103   21
     clus
vv    PNPLA4 MUTATED PNPLA4 WILD-TYPE
  NO               5              103
  YES              0               21
[1] 2 2
[1] FALSE
D8V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PNPLA4 MUTATED       0                         0     4
  PNPLA4 WILD-TYPE     4                         6   112
D8V9, multiclass
                           clus
vv                          PNPLA4 MUTATED PNPLA4 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D8V10, binary
                  cls
clus                 0   1
  PNPLA4 MUTATED     1   3
  PNPLA4 WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA4 MUTATED      1    3
  PNPLA4 WILD-TYPE   11  106
                        clus
vv                       PNPLA4 MUTATED PNPLA4 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(9) Variable = SERINC2 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  SERINC2 MUTATED     3   0
  SERINC2 WILD-TYPE 124   4
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               128 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                0                 4 
$`SERINC2 MUTATED`
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAHN 
       84.99        89.88       211.89 

$`SERINC2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       73.45        80.19        81.47        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
      182.10        59.80       232.80       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  SERINC2 MUTATED SERINC2 WILD-TYPE 
            84.99              0.10 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
           211.89            244.50 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
            89.88             40.70 
[1] "85.0 - 211.9 (89.9)" "0.1 - 244.5 (40.7)" 
[1] "hr="     "9300000"
D9V2, continuous
                   vv
clus                IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERINC2 MUTATED    2       1        0        0        0         0         0
  SERINC2 WILD-TYPE 44      17       25       11        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SERINC2 MUTATED           0         0          0          0          0
  SERINC2 WILD-TYPE         1         2          1          6          5
D9V3, multiclass
            clus
vv           SERINC2 MUTATED SERINC2 WILD-TYPE
  IS                       2                44
  STAGE I                  1                17
  STAGE IA                 0                25
  STAGE IB                 0                11
  STAGE II                 0                 4
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
[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                T1 T2 T3
  SERINC2 MUTATED    2  1  0
  SERINC2 WILD-TYPE 72 49  6
D9V4, multiclass
    clus
vv   SERINC2 MUTATED SERINC2 WILD-TYPE
  T1               2                72
  T2               1                49
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  SERINC2 MUTATED    3     0
  SERINC2 WILD-TYPE 42    12
D9V5, multiclass
       clus
vv      SERINC2 MUTATED SERINC2 WILD-TYPE
  N0                  3                42
  N1+N2               0                12
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  SERINC2 MUTATED     3   0
  SERINC2 WILD-TYPE 110   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERINC2 MUTATED      3    0
  SERINC2 WILD-TYPE  110    4
   clus
vv  SERINC2 MUTATED SERINC2 WILD-TYPE
  0               3               110
  1               0                 4
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  SERINC2 MUTATED     2   1
  SERINC2 WILD-TYPE 106  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERINC2 MUTATED      2    1
  SERINC2 WILD-TYPE  106   20
     clus
vv    SERINC2 MUTATED SERINC2 WILD-TYPE
  NO                2               106
  YES               1                20
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERINC2 MUTATED       0                         0     3
  SERINC2 WILD-TYPE     4                         6   113
D9V9, multiclass
                           clus
vv                          SERINC2 MUTATED SERINC2 WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3               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"
D9V10, binary
                   cls
clus                  0   1
  SERINC2 MUTATED     0   3
  SERINC2 WILD-TYPE  12 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERINC2 MUTATED      0    3
  SERINC2 WILD-TYPE   12  106
                        clus
vv                       SERINC2 MUTATED SERINC2 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3               106
[1] 2 2
[1] FALSE

Clustering(10) Variable = RHPN2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  RHPN2 MUTATED     5   1
  RHPN2 WILD-TYPE 122   3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             125 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              1               3 
$`RHPN2 MUTATED`
TCGA-2G-AAEW TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAHG TCGA-2G-AAKL TCGA-YU-A90W 
       20.32        44.48        75.58        59.80       230.89        36.59 

$`RHPN2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84       103.13        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      199.23        59.90       204.16        73.91       110.10       182.10 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      225.60       229.22       244.50       131.21        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
       19.96        14.33        17.03         0.10        15.88        22.95 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        17.75        37.18        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 
        9.24        68.02        64.57        31.92         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  RHPN2 MUTATED RHPN2 WILD-TYPE 
          20.32            0.10 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         230.89          244.50 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
          52.14           41.39 
[1] "20.3 - 230.9 (52.1)" "0.1 - 244.5 (41.4)" 
[1] "hr=" "3.3"
D10V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHPN2 MUTATED    2       1        1        0        1         0         0
  RHPN2 WILD-TYPE 44      17       24       11        3         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RHPN2 MUTATED           0         1          0          0          0
  RHPN2 WILD-TYPE         1         1          1          6          5
D10V3, multiclass
            clus
vv           RHPN2 MUTATED RHPN2 WILD-TYPE
  IS                     2              44
  STAGE I                1              17
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              1               1
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  RHPN2 MUTATED    4  1  1
  RHPN2 WILD-TYPE 70 49  5
D10V4, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  T1             4              70
  T2             1              49
  T3             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  RHPN2 MUTATED    3     0
  RHPN2 WILD-TYPE 42    12
D10V5, multiclass
       clus
vv      RHPN2 MUTATED RHPN2 WILD-TYPE
  N0                3              42
  N1+N2             0              12
[1] 2 2
[1] FALSE
D10V6, binary
                 cls
clus                0   1
  RHPN2 MUTATED     4   1
  RHPN2 WILD-TYPE 109   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      4    1
  RHPN2 WILD-TYPE  109    3
   clus
vv  RHPN2 MUTATED RHPN2 WILD-TYPE
  0             4             109
  1             1               3
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  RHPN2 MUTATED     4   2
  RHPN2 WILD-TYPE 104  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      4    2
  RHPN2 WILD-TYPE  104   19
     clus
vv    RHPN2 MUTATED RHPN2 WILD-TYPE
  NO              4             104
  YES             2              19
[1] 2 2
[1] FALSE
D10V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHPN2 MUTATED       0                         0     6
  RHPN2 WILD-TYPE     4                         6   110
D10V9, multiclass
                           clus
vv                          RHPN2 MUTATED RHPN2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 6             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"
D10V10, binary
                 cls
clus                0   1
  RHPN2 MUTATED     0   5
  RHPN2 WILD-TYPE  12 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      0    5
  RHPN2 WILD-TYPE   12  104
                        clus
vv                       RHPN2 MUTATED RHPN2 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             5             104
[1] 2 2
[1] FALSE

Clustering(11) Variable = RBM10 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED     4   0
  RBM10 WILD-TYPE 123   4
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             127 
  RBM10 MUTATED RBM10 WILD-TYPE 
              0               4 
$`RBM10 MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAH0 TCGA-2G-AAL5 
       76.11       128.58       180.07       244.50 

$`RBM10 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      114.77       203.28        45.21        22.19        26.04        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        25.41        22.52        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      199.23        59.90       204.16        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP 
      216.92       225.60       230.89       229.22       131.21        86.96 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       14.30        19.96        14.33        17.03         0.10        15.88 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       22.95        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  RBM10 MUTATED RBM10 WILD-TYPE 
          76.11            0.10 
  RBM10 MUTATED RBM10 WILD-TYPE 
          244.5           232.8 
  RBM10 MUTATED RBM10 WILD-TYPE 
        154.325          40.010 
[1] "76.1 - 244.5 (154.3)" "0.1 - 232.8 (40.0)"  
[1] "hr="     "9.2e+07"
D11V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM10 MUTATED    1       2        1        0        0         0         0
  RBM10 WILD-TYPE 45      16       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RBM10 MUTATED           0         0          0          0          0
  RBM10 WILD-TYPE         1         2          1          6          5
D11V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  IS                     1              45
  STAGE I                2              16
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  RBM10 MUTATED    3  1  0
  RBM10 WILD-TYPE 71 49  6
D11V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             3              71
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  RBM10 MUTATED    3     0
  RBM10 WILD-TYPE 42    12
D11V5, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  N0                3              42
  N1+N2             0              12
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus                0   1
  RBM10 MUTATED     4   0
  RBM10 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4    0
  RBM10 WILD-TYPE  109    4
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  RBM10 MUTATED     2   2
  RBM10 WILD-TYPE 106  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE  106   19
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              2             106
  YES             2              19
[1] 2 2
[1] FALSE
D11V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       0                         0     4
  RBM10 WILD-TYPE     4                         6   112
D11V9, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D11V10, binary
                 cls
clus                0   1
  RBM10 MUTATED     0   4
  RBM10 WILD-TYPE  12 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0    4
  RBM10 WILD-TYPE   12  105
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(12) Variable = HSF4 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  HSF4 MUTATED     6   0
  HSF4 WILD-TYPE 121   4
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            125 
  HSF4 MUTATED HSF4 WILD-TYPE 
             0              4 
$`HSF4 MUTATED`
TCGA-2G-AAFM TCGA-2G-AAH0 TCGA-2G-AAHA TCGA-2G-AAKG TCGA-XE-AAOD TCGA-YU-A90S 
       16.54       180.07       110.10       216.92        67.66        31.92 

$`HSF4 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       26.04        24.66        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC 
      172.04       199.23        59.90       204.16        73.91       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      225.60       230.89       229.22       244.50       131.21        86.96 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       14.30        19.96        14.33        17.03         0.10        15.88 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       22.95        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        9.24        68.02        64.57        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  HSF4 MUTATED HSF4 WILD-TYPE 
         16.54           0.10 
  HSF4 MUTATED HSF4 WILD-TYPE 
        216.92         244.50 
  HSF4 MUTATED HSF4 WILD-TYPE 
         88.88          41.39 
[1] "16.5 - 216.9 (88.9)" "0.1 - 244.5 (41.4)" 
[1] "hr="     "2.6e+07"
D12V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSF4 MUTATED    1       1        1        2        0         1         0
  HSF4 WILD-TYPE 45      17       24        9        4         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HSF4 MUTATED           0         0          0          0          0
  HSF4 WILD-TYPE         1         2          1          6          5
D12V3, multiclass
            clus
vv           HSF4 MUTATED HSF4 WILD-TYPE
  IS                    1             45
  STAGE I               1             17
  STAGE IA              1             24
  STAGE IB              2              9
  STAGE II              0              4
  STAGE IIA             1              4
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  HSF4 MUTATED    2  4  0
  HSF4 WILD-TYPE 72 46  6
D12V4, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  T1            2             72
  T2            4             46
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  HSF4 MUTATED    1     1
  HSF4 WILD-TYPE 44    11
D12V5, multiclass
[1] "Remove cluster labels:" "HSF4 MUTATED"          
clus
  HSF4 MUTATED HSF4 WILD-TYPE 
             2             55 
    TCGA-2G-AAG0     TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAF4     TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAFH     TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAFN     TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAG5     TCGA-2G-AAG6     TCGA-2G-AAG7     TCGA-2G-AAG8 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAG9     TCGA-2G-AAGA     TCGA-2G-AAGC     TCGA-2G-AAGE 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAGF     TCGA-2G-AAGG     TCGA-2G-AAGI     TCGA-2G-AAGJ 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAGK     TCGA-2G-AAGM     TCGA-2G-AAGN     TCGA-2G-AAGO 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAGP     TCGA-2G-AAGS     TCGA-2G-AAGW     TCGA-2G-AAGX 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAGY     TCGA-2G-AAGZ     TCGA-2G-AAH2     TCGA-2G-AAHG 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAHL     TCGA-2G-AAHN     TCGA-2G-AAHP     TCGA-2G-AAHT 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAL5     TCGA-2G-AAL7     TCGA-4K-AA1G     TCGA-4K-AA1H 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-4K-AA1I     TCGA-4K-AAAL     TCGA-SO-A8JP     TCGA-VF-A8A8 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VF-A8AA     TCGA-VF-A8AB     TCGA-X3-A8G4 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
D12V6, binary
                cls
clus               0   1
  HSF4 MUTATED     5   0
  HSF4 WILD-TYPE 108   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      5    0
  HSF4 WILD-TYPE  108    4
   clus
vv  HSF4 MUTATED HSF4 WILD-TYPE
  0            5            108
  1            0              4
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  HSF4 MUTATED     5   1
  HSF4 WILD-TYPE 103  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      5    1
  HSF4 WILD-TYPE  103   20
     clus
vv    HSF4 MUTATED HSF4 WILD-TYPE
  NO             5            103
  YES            1             20
[1] 2 2
[1] FALSE
D12V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSF4 MUTATED       0                         0     6
  HSF4 WILD-TYPE     4                         6   110
D12V9, multiclass
                           clus
vv                          HSF4 MUTATED HSF4 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                6            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"
D12V10, binary
                cls
clus               0   1
  HSF4 MUTATED     0   5
  HSF4 WILD-TYPE  12 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      0    5
  HSF4 WILD-TYPE   12  104
                        clus
vv                       HSF4 MUTATED HSF4 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(13) Variable = CDC27 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED     6   0
  CDC27 WILD-TYPE 121   4
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             125 
  CDC27 MUTATED CDC27 WILD-TYPE 
              0               4 
$`CDC27 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAFH TCGA-2G-AAG8 TCGA-2G-AAHP TCGA-4K-AA1I TCGA-XE-AAOL 
       41.39        45.21        75.25       186.31         0.10         0.43 

$`CDC27 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        20.32        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      114.77       128.58       203.28        22.19        26.04        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        25.41        22.52        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       75.58        73.35        81.37        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84       103.13        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      199.23        59.90       204.16        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80       232.80       211.89        17.82       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      225.60       230.89       229.22       244.50       131.21        86.96 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW 
       14.30        19.96        14.33        17.03        15.88        22.95 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        17.75        37.18        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69        50.96        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       68.02        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.10            0.46 
  CDC27 MUTATED CDC27 WILD-TYPE 
         186.31          244.50 
  CDC27 MUTATED CDC27 WILD-TYPE 
          43.30           41.52 
[1] "0.1 - 186.3 (43.3)" "0.5 - 244.5 (41.5)"
[1] "hr="     "2.6e+07"
D13V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC27 MUTATED    2       1        1        1        0         0         1
  CDC27 WILD-TYPE 44      17       24       10        4         5         0
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDC27 MUTATED           0         0          0          0          0
  CDC27 WILD-TYPE         1         2          1          6          5
D13V3, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  IS                     2              44
  STAGE I                1              17
  STAGE IA               1              24
  STAGE IB               1              10
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              1               0
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  CDC27 MUTATED    4  2  0
  CDC27 WILD-TYPE 70 48  6
D13V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             4              70
  T2             2              48
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  CDC27 MUTATED    4     1
  CDC27 WILD-TYPE 41    11
D13V5, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  N0                4              41
  N1+N2             1              11
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus                0   1
  CDC27 MUTATED     6   0
  CDC27 WILD-TYPE 107   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      6    0
  CDC27 WILD-TYPE  107    4
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             6             107
  1             0               4
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  CDC27 MUTATED     3   2
  CDC27 WILD-TYPE 105  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    2
  CDC27 WILD-TYPE  105   19
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              3             105
  YES             2              19
[1] 2 2
[1] FALSE
D13V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         1     5
  CDC27 WILD-TYPE     4                         5   111
D13V9, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 5             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"
D13V10, binary
                 cls
clus                0   1
  CDC27 MUTATED     0   6
  CDC27 WILD-TYPE  12 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    6
  CDC27 WILD-TYPE   12  103
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             6             103
[1] 2 2
[1] FALSE

Clustering(14) Variable = MLLT3 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  MLLT3 MUTATED     3   0
  MLLT3 WILD-TYPE 124   4
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             128 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              0               4 
$`MLLT3 MUTATED`
TCGA-2G-AAHN TCGA-2G-AAKH TCGA-SN-A84Y 
      211.89       225.60        17.23 

$`MLLT3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP 
       73.91       110.10       182.10        59.80       232.80       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       216.92       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  MLLT3 MUTATED MLLT3 WILD-TYPE 
          17.23            0.10 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
          225.6           244.5 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
        211.890          41.455 
[1] "17.2 - 225.6 (211.9)" "0.1 - 244.5 (41.5)"  
[1] "hr="     "9200000"
D14V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLLT3 MUTATED    1       1        0        0        1         0         0
  MLLT3 WILD-TYPE 45      17       25       11        3         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MLLT3 MUTATED           0         0          0          0          0
  MLLT3 WILD-TYPE         1         2          1          6          5
D14V3, multiclass
            clus
vv           MLLT3 MUTATED MLLT3 WILD-TYPE
  IS                     1              45
  STAGE I                1              17
  STAGE IA               0              25
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  MLLT3 MUTATED    2  1  0
  MLLT3 WILD-TYPE 72 49  6
D14V4, multiclass
    clus
vv   MLLT3 MUTATED MLLT3 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  MLLT3 MUTATED    1     0
  MLLT3 WILD-TYPE 44    12
D14V5, multiclass
[1] "Remove cluster labels:" "MLLT3 MUTATED"         
clus
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              1              56 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGW 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHP      TCGA-2G-AAHT 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-4K-AA1H      TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-VF-A8A8      TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
D14V6, binary
                 cls
clus                0   1
  MLLT3 MUTATED     3   0
  MLLT3 WILD-TYPE 110   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT3 MUTATED      3    0
  MLLT3 WILD-TYPE  110    4
   clus
vv  MLLT3 MUTATED MLLT3 WILD-TYPE
  0             3             110
  1             0               4
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus                0   1
  MLLT3 MUTATED     2   1
  MLLT3 WILD-TYPE 106  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT3 MUTATED      2    1
  MLLT3 WILD-TYPE  106   20
     clus
vv    MLLT3 MUTATED MLLT3 WILD-TYPE
  NO              2             106
  YES             1              20
[1] 2 2
[1] FALSE
D14V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLLT3 MUTATED       0                         0     3
  MLLT3 WILD-TYPE     4                         6   113
D14V9, multiclass
                           clus
vv                          MLLT3 MUTATED MLLT3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D14V10, binary
                 cls
clus                0   1
  MLLT3 MUTATED     1   2
  MLLT3 WILD-TYPE  11 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT3 MUTATED      1    2
  MLLT3 WILD-TYPE   11  107
                        clus
vv                       MLLT3 MUTATED MLLT3 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(15) Variable = ERC1 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  ERC1 MUTATED     6   0
  ERC1 WILD-TYPE 121   4
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            125 
  ERC1 MUTATED ERC1 WILD-TYPE 
             0              4 
$`ERC1 MUTATED`
TCGA-2G-AAG8 TCGA-2G-AAGN TCGA-2G-AAH8 TCGA-4K-AA1I TCGA-WZ-A8D5 TCGA-XE-AANI 
       75.25       120.20        73.91         0.10        25.45        34.22 

$`ERC1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 
       36.13        44.48        75.58        73.35        81.37        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       96.59       119.05       127.92       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC 
      180.07       199.23        59.90       204.16       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AAAL 
       86.96        14.30        19.96        14.33        17.03        15.88 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       22.95        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       24.76        29.39        34.88        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        23.28        65.98         0.46        55.92        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       12.07         7.89        16.87         8.88        67.66        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       68.02        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        22.39        57.07        20.84 

  ERC1 MUTATED ERC1 WILD-TYPE 
          0.10           0.43 
  ERC1 MUTATED ERC1 WILD-TYPE 
         120.2          244.5 
  ERC1 MUTATED ERC1 WILD-TYPE 
        54.065         41.520 
[1] "0.1 - 120.2 (54.1)" "0.4 - 244.5 (41.5)"
[1] "hr="     "2.6e+07"
D15V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERC1 MUTATED    1       0        1        1        0         0         0
  ERC1 WILD-TYPE 45      18       24       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ERC1 MUTATED           0         0          0          1          1
  ERC1 WILD-TYPE         1         2          1          5          4
D15V3, multiclass
            clus
vv           ERC1 MUTATED ERC1 WILD-TYPE
  IS                    1             45
  STAGE I               0             18
  STAGE IA              1             24
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            1              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             T1 T2 T3
  ERC1 MUTATED    2  3  1
  ERC1 WILD-TYPE 72 47  5
D15V4, multiclass
    clus
vv   ERC1 MUTATED ERC1 WILD-TYPE
  T1            2             72
  T2            3             47
  T3            1              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  ERC1 MUTATED    2     1
  ERC1 WILD-TYPE 43    11
D15V5, multiclass
       clus
vv      ERC1 MUTATED ERC1 WILD-TYPE
  N0               2             43
  N1+N2            1             11
[1] 2 2
[1] FALSE
D15V6, binary
                cls
clus               0   1
  ERC1 MUTATED     6   0
  ERC1 WILD-TYPE 107   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC1 MUTATED      6    0
  ERC1 WILD-TYPE  107    4
   clus
vv  ERC1 MUTATED ERC1 WILD-TYPE
  0            6            107
  1            0              4
[1] 2 2
[1] FALSE
D15V7, binary
                cls
clus               0   1
  ERC1 MUTATED     5   1
  ERC1 WILD-TYPE 103  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC1 MUTATED      5    1
  ERC1 WILD-TYPE  103   20
     clus
vv    ERC1 MUTATED ERC1 WILD-TYPE
  NO             5            103
  YES            1             20
[1] 2 2
[1] FALSE
D15V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERC1 MUTATED       0                         0     6
  ERC1 WILD-TYPE     4                         6   110
D15V9, multiclass
                           clus
vv                          ERC1 MUTATED ERC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                6            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"
D15V10, binary
                cls
clus               0   1
  ERC1 MUTATED     0   6
  ERC1 WILD-TYPE  12 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC1 MUTATED      0    6
  ERC1 WILD-TYPE   12  103
                        clus
vv                       ERC1 MUTATED ERC1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            6            103
[1] 2 2
[1] FALSE

Clustering(16) Variable = SP8 MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  SP8 MUTATED     4   0
  SP8 WILD-TYPE 123   4
  SP8 MUTATED SP8 WILD-TYPE 
            4           127 
  SP8 MUTATED SP8 WILD-TYPE 
            0             4 
$`SP8 MUTATED`
TCGA-2G-AAFI TCGA-2G-AAGA TCGA-SN-A84X TCGA-XE-AANI 
       22.19        80.19        10.26        34.22 

$`SP8 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ 
       76.11       114.77       128.58       203.28        45.21        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38        16.31         9.63        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        23.28        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  SP8 MUTATED SP8 WILD-TYPE 
        10.26          0.10 
  SP8 MUTATED SP8 WILD-TYPE 
        80.19        244.50 
  SP8 MUTATED SP8 WILD-TYPE 
       28.205        41.690 
[1] "10.3 - 80.2 (28.2)" "0.1 - 244.5 (41.7)"
[1] "hr="     "2.5e+07"
D16V2, continuous
               vv
clus            IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP8 MUTATED    2       0        0        1        0         1         0
  SP8 WILD-TYPE 44      18       25       10        4         4         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SP8 MUTATED           0         0          0          0          0
  SP8 WILD-TYPE         1         2          1          6          5
D16V3, multiclass
            clus
vv           SP8 MUTATED SP8 WILD-TYPE
  IS                   2            44
  STAGE I              0            18
  STAGE IA             0            25
  STAGE IB             1            10
  STAGE II             0             4
  STAGE IIA            1             4
  STAGE IIB            0             1
  STAGE IIC            0             1
  STAGE III            0             2
  STAGE IIIA           0             1
  STAGE IIIB           0             6
  STAGE IIIC           0             5
[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            T1 T2 T3
  SP8 MUTATED    2  2  0
  SP8 WILD-TYPE 72 48  6
D16V4, multiclass
    clus
vv   SP8 MUTATED SP8 WILD-TYPE
  T1           2            72
  T2           2            48
  T3           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  SP8 MUTATED    1     1
  SP8 WILD-TYPE 44    11
D16V5, multiclass
[1] "Remove cluster labels:" "SP8 MUTATED"           
clus
  SP8 MUTATED SP8 WILD-TYPE 
            2            55 
   TCGA-2G-AAG0    TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAF6    TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFJ 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAFY    TCGA-2G-AAG5    TCGA-2G-AAG6    TCGA-2G-AAG7    TCGA-2G-AAG8 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAG9    TCGA-2G-AAGC    TCGA-2G-AAGE    TCGA-2G-AAGF    TCGA-2G-AAGG 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAGI    TCGA-2G-AAGJ    TCGA-2G-AAGK    TCGA-2G-AAGM    TCGA-2G-AAGN 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAGO    TCGA-2G-AAGP    TCGA-2G-AAGS    TCGA-2G-AAGW    TCGA-2G-AAGX 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH2    TCGA-2G-AAHG    TCGA-2G-AAHL 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT    TCGA-2G-AAKG    TCGA-2G-AAL5 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAL7    TCGA-4K-AA1G    TCGA-4K-AA1H    TCGA-4K-AA1I    TCGA-4K-AAAL 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-SO-A8JP    TCGA-VF-A8A8    TCGA-VF-A8AA    TCGA-VF-A8AB    TCGA-X3-A8G4 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
D16V6, binary
               cls
clus              0   1
  SP8 MUTATED     4   0
  SP8 WILD-TYPE 109   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP8 MUTATED      4    0
  SP8 WILD-TYPE  109    4
   clus
vv  SP8 MUTATED SP8 WILD-TYPE
  0           4           109
  1           0             4
[1] 2 2
[1] FALSE
D16V7, binary
               cls
clus              0   1
  SP8 MUTATED     4   0
  SP8 WILD-TYPE 104  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP8 MUTATED      4    0
  SP8 WILD-TYPE  104   21
     clus
vv    SP8 MUTATED SP8 WILD-TYPE
  NO            4           104
  YES           0            21
[1] 2 2
[1] FALSE
D16V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP8 MUTATED       0                         0     4
  SP8 WILD-TYPE     4                         6   112
D16V9, multiclass
                           clus
vv                          SP8 MUTATED SP8 WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               4           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"
D16V10, binary
               cls
clus              0   1
  SP8 MUTATED     1   3
  SP8 WILD-TYPE  11 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP8 MUTATED      1    3
  SP8 WILD-TYPE   11  106
                        clus
vv                       SP8 MUTATED SP8 WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(17) Variable = NAT10 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  NAT10 MUTATED     4   0
  NAT10 WILD-TYPE 123   4
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             127 
  NAT10 MUTATED NAT10 WILD-TYPE 
              0               4 
$`NAT10 MUTATED`
TCGA-2G-AAGM TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-VF-A8A8 
      127.92        13.58        16.31        37.18 

$`NAT10 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
      103.13        96.59       119.05       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA 
        1.38         9.63        10.26        17.23        17.75        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  NAT10 MUTATED NAT10 WILD-TYPE 
          13.58            0.10 
  NAT10 MUTATED NAT10 WILD-TYPE 
         127.92          244.50 
  NAT10 MUTATED NAT10 WILD-TYPE 
         26.745          41.690 
[1] "13.6 - 127.9 (26.7)" "0.1 - 244.5 (41.7)" 
[1] "hr="     "9200000"
D17V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAT10 MUTATED    2       0        2        0        0         0         0
  NAT10 WILD-TYPE 44      18       23       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NAT10 MUTATED           0         0          0          0          0
  NAT10 WILD-TYPE         1         2          1          6          5
D17V3, multiclass
            clus
vv           NAT10 MUTATED NAT10 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               2              23
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  NAT10 MUTATED    3  1  0
  NAT10 WILD-TYPE 71 49  6
D17V4, multiclass
    clus
vv   NAT10 MUTATED NAT10 WILD-TYPE
  T1             3              71
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  NAT10 MUTATED    2     0
  NAT10 WILD-TYPE 43    12
D17V5, multiclass
[1] "Remove cluster labels:" "NAT10 MUTATED"         
clus
  NAT10 MUTATED NAT10 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGN      TCGA-2G-AAGO 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGW      TCGA-2G-AAGX 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-4K-AA1H      TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
D17V6, binary
                 cls
clus                0   1
  NAT10 MUTATED     4   0
  NAT10 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAT10 MUTATED      4    0
  NAT10 WILD-TYPE  109    4
   clus
vv  NAT10 MUTATED NAT10 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  NAT10 MUTATED     4   0
  NAT10 WILD-TYPE 104  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAT10 MUTATED      4    0
  NAT10 WILD-TYPE  104   21
     clus
vv    NAT10 MUTATED NAT10 WILD-TYPE
  NO              4             104
  YES             0              21
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "NAT10 MUTATED"         
clus
  NAT10 MUTATED NAT10 WILD-TYPE 
              2              99 
     TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-ZM-AA0E      TCGA-2G-AAEX 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAF1      TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFG      TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFL      TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFV      TCGA-2G-AAFY      TCGA-2G-AAFZ      TCGA-2G-AAG5 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8      TCGA-2G-AAG9 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE      TCGA-2G-AAGF 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGT      TCGA-2G-AAGV      TCGA-2G-AAGW      TCGA-2G-AAGX 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH0      TCGA-2G-AAH2 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAH3      TCGA-2G-AAH4      TCGA-2G-AAH8      TCGA-2G-AAHA 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAHC      TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHN 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKD      TCGA-2G-AAKG 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAKH      TCGA-2G-AAKL      TCGA-2G-AAKM      TCGA-2G-AAL5 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAL7      TCGA-2G-AALP      TCGA-2X-A9D5      TCGA-2X-A9D6 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AAAL      TCGA-S6-A8JW 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-S6-A8JX      TCGA-SB-A76C      TCGA-SN-A84Y      TCGA-SO-A8JP 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-WZ-A7V3      TCGA-WZ-A7V4      TCGA-WZ-A7V5      TCGA-WZ-A8D5 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-XE-A8H1      TCGA-XE-A8H4      TCGA-XE-A8H5      TCGA-XE-A9SE 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-XE-AANI      TCGA-XE-AANJ      TCGA-XE-AANR      TCGA-XE-AANV 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-XE-AAO3      TCGA-XE-AAO4      TCGA-XE-AAO6      TCGA-XE-AAOC 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-XE-AAOD      TCGA-XE-AAOF      TCGA-XE-AAOJ      TCGA-XE-AAOL 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-ZM-AA05      TCGA-ZM-AA06      TCGA-ZM-AA0B      TCGA-ZM-AA0D 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAT10 MUTATED       0                         0     4
  NAT10 WILD-TYPE     4                         6   112
D17V9, multiclass
                           clus
vv                          NAT10 MUTATED NAT10 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D17V10, binary
                 cls
clus                0   1
  NAT10 MUTATED     1   3
  NAT10 WILD-TYPE  11 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAT10 MUTATED      1    3
  NAT10 WILD-TYPE   11  106
                        clus
vv                       NAT10 MUTATED NAT10 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(18) Variable = SPIN2A MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  SPIN2A MUTATED     3   0
  SPIN2A WILD-TYPE 124   4
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              128 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               0                4 
$`SPIN2A MUTATED`
TCGA-2G-AAGK TCGA-SN-A6IS TCGA-SN-A84W 
      119.05        16.31         9.63 

$`SPIN2A WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
      103.13        96.59       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       13.58         1.38        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  SPIN2A MUTATED SPIN2A WILD-TYPE 
            9.63             0.10 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
          119.05           244.50 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
          16.310           41.605 
[1] "9.6 - 119.0 (16.3)" "0.1 - 244.5 (41.6)"
[1] "hr="     "9100000"
D18V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPIN2A MUTATED    3       0        0        0        0         0         0
  SPIN2A WILD-TYPE 43      18       25       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SPIN2A MUTATED           0         0          0          0          0
  SPIN2A WILD-TYPE         1         2          1          6          5
D18V3, multiclass
            clus
vv           SPIN2A MUTATED SPIN2A WILD-TYPE
  IS                      3               43
  STAGE I                 0               18
  STAGE IA                0               25
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  SPIN2A MUTATED    1  2  0
  SPIN2A WILD-TYPE 73 48  6
D18V4, multiclass
    clus
vv   SPIN2A MUTATED SPIN2A WILD-TYPE
  T1              1               73
  T2              2               48
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  SPIN2A MUTATED    1     0
  SPIN2A WILD-TYPE 44    12
D18V5, multiclass
[1] "Remove cluster labels:" "SPIN2A MUTATED"        
clus
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               1               56 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFY       TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGJ       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
D18V6, binary
                  cls
clus                 0   1
  SPIN2A MUTATED     3   0
  SPIN2A WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIN2A MUTATED      3    0
  SPIN2A WILD-TYPE  110    4
   clus
vv  SPIN2A MUTATED SPIN2A WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  SPIN2A MUTATED     3   0
  SPIN2A WILD-TYPE 105  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIN2A MUTATED      3    0
  SPIN2A WILD-TYPE  105   21
     clus
vv    SPIN2A MUTATED SPIN2A WILD-TYPE
  NO               3              105
  YES              0               21
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "SPIN2A MUTATED"        
clus
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               1              100 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEX 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGM 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP       TCGA-2G-AAGS 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW       TCGA-2G-AAGX 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0       TCGA-2G-AAH2 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8       TCGA-2G-AAHA 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AAAL       TCGA-S6-A8JW 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-S6-A8JX       TCGA-SB-A6J6       TCGA-SB-A76C       TCGA-SN-A84Y 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-SO-A8JP       TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-WZ-A8D5       TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-XE-A9SE       TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-XE-AANV       TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-XE-AAOC       TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-XE-AAOL       TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-ZM-AA0D       TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPIN2A MUTATED       0                         0     3
  SPIN2A WILD-TYPE     4                         6   113
D18V9, multiclass
                           clus
vv                          SPIN2A MUTATED SPIN2A WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D18V10, binary
                  cls
clus                 0   1
  SPIN2A MUTATED     2   1
  SPIN2A WILD-TYPE  10 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIN2A MUTATED      2    1
  SPIN2A WILD-TYPE   10  108
                        clus
vv                       SPIN2A MUTATED SPIN2A WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              1              108
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEK MUTATION ANALYSIS
D19V1, survival
               sevent
clus2             0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 122   4
  DEK MUTATED DEK WILD-TYPE 
            5           126 
  DEK MUTATED DEK WILD-TYPE 
            0             4 
$`DEK MUTATED`
TCGA-2G-AAFG TCGA-2G-AAGC TCGA-2G-AAHP TCGA-W4-A7U2 TCGA-XE-A8H5 
      203.28        84.99       186.31        41.52        40.01 

$`DEK WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
       76.11       114.77       128.58        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       80.19        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD 
      182.10        59.80       232.80       211.89        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U4 
       37.68        24.99        35.61        33.07        23.90        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  DEK MUTATED DEK WILD-TYPE 
        40.01          0.10 
  DEK MUTATED DEK WILD-TYPE 
       203.28        244.50 
  DEK MUTATED DEK WILD-TYPE 
       84.990        39.535 
[1] "40.0 - 203.3 (85.0)" "0.1 - 244.5 (39.5)" 
[1] "hr="     "2.6e+07"
D19V2, continuous
               vv
clus            IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DEK MUTATED    4       0        0        0        0         0         0
  DEK WILD-TYPE 42      18       25       11        4         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEK MUTATED           0         0          0          0          0
  DEK WILD-TYPE         1         2          1          6          5
D19V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  IS                   4            42
  STAGE I              0            18
  STAGE IA             0            25
  STAGE IB             0            11
  STAGE II             0             4
  STAGE IIA            0             5
  STAGE IIB            0             1
  STAGE IIC            0             1
  STAGE III            0             2
  STAGE IIIA           0             1
  STAGE IIIB           0             6
  STAGE IIIC           0             5
[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            T1 T2 T3
  DEK MUTATED    4  1  0
  DEK WILD-TYPE 70 49  6
D19V4, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           4            70
  T2           1            49
  T3           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  DEK MUTATED    3     0
  DEK WILD-TYPE 42    12
D19V5, multiclass
       clus
vv      DEK MUTATED DEK WILD-TYPE
  N0              3            42
  N1+N2           0            12
[1] 2 2
[1] FALSE
D19V6, binary
               cls
clus              0   1
  DEK MUTATED     4   0
  DEK WILD-TYPE 109   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    0
  DEK WILD-TYPE  109    4
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           4           109
  1           0             4
[1] 2 2
[1] FALSE
D19V7, binary
               cls
clus              0   1
  DEK MUTATED     2   3
  DEK WILD-TYPE 106  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      2    3
  DEK WILD-TYPE  106   18
     clus
vv    DEK MUTATED DEK WILD-TYPE
  NO            2           106
  YES           3            18
[1] 2 2
[1] FALSE
D19V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEK MUTATED       0                         0     4
  DEK WILD-TYPE     4                         6   112
D19V9, multiclass
                           clus
vv                          DEK MUTATED DEK WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               4           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"
D19V10, binary
               cls
clus              0   1
  DEK MUTATED     1   4
  DEK WILD-TYPE  11 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      1    4
  DEK WILD-TYPE   11  105
                        clus
vv                       DEK MUTATED DEK WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO           4           105
[1] 2 2
[1] FALSE

Clustering(20) Variable = FANK1 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  FANK1 MUTATED     4   0
  FANK1 WILD-TYPE 123   4
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             127 
  FANK1 MUTATED FANK1 WILD-TYPE 
              0               4 
$`FANK1 MUTATED`
TCGA-2G-AAFN TCGA-2G-AAKL TCGA-WZ-A8D5 TCGA-XE-A8H5 
       25.41       230.89        25.45        40.01 

$`FANK1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       26.04        24.66        16.54        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       216.92       225.60       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 
       41.52        24.26        24.76        29.39        34.88        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  FANK1 MUTATED FANK1 WILD-TYPE 
          25.41            0.10 
  FANK1 MUTATED FANK1 WILD-TYPE 
         230.89          244.50 
  FANK1 MUTATED FANK1 WILD-TYPE 
          32.73           41.69 
[1] "25.4 - 230.9 (32.7)" "0.1 - 244.5 (41.7)" 
[1] "hr="     "9.2e+07"
D20V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FANK1 MUTATED    1       0        0        0        1         0         0
  FANK1 WILD-TYPE 45      18       25       11        3         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FANK1 MUTATED           0         0          0          1          0
  FANK1 WILD-TYPE         1         2          1          5          5
D20V3, multiclass
            clus
vv           FANK1 MUTATED FANK1 WILD-TYPE
  IS                     1              45
  STAGE I                0              18
  STAGE IA               0              25
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             1               5
  STAGE IIIC             0               5
[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              T1 T2 T3
  FANK1 MUTATED    1  2  1
  FANK1 WILD-TYPE 73 48  5
D20V4, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  T1             1              73
  T2             2              48
  T3             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  FANK1 MUTATED    0     1
  FANK1 WILD-TYPE 45    11
D20V5, multiclass
[1] "Remove cluster labels:" "FANK1 MUTATED"         
clus
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              56 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGW      TCGA-2G-AAGX 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-4K-AA1H      TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-VF-A8A8      TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
D20V6, binary
                 cls
clus                0   1
  FANK1 MUTATED     4   0
  FANK1 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      4    0
  FANK1 WILD-TYPE  109    4
   clus
vv  FANK1 MUTATED FANK1 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D20V7, binary
                 cls
clus                0   1
  FANK1 MUTATED     2   2
  FANK1 WILD-TYPE 106  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      2    2
  FANK1 WILD-TYPE  106   19
     clus
vv    FANK1 MUTATED FANK1 WILD-TYPE
  NO              2             106
  YES             2              19
[1] 2 2
[1] FALSE
D20V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FANK1 MUTATED       0                         0     3
  FANK1 WILD-TYPE     4                         6   113
D20V9, multiclass
                           clus
vv                          FANK1 MUTATED FANK1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D20V10, binary
                 cls
clus                0   1
  FANK1 MUTATED     1   3
  FANK1 WILD-TYPE  11 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      1    3
  FANK1 WILD-TYPE   11  106
                        clus
vv                       FANK1 MUTATED FANK1 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(21) Variable = ANKRD11 MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2                 0   1
  ANKRD11 MUTATED     5   0
  ANKRD11 WILD-TYPE 122   4
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               126 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                0                 4 
$`ANKRD11 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAHA TCGA-VF-A8AB TCGA-XE-AAO3 TCGA-YU-A90S 
       41.39       110.10        24.99        93.93        31.92 

$`ANKRD11 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        20.32        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        37.68        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
        0.46        55.92        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y 
       27.72         9.24        68.02        64.57        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
            24.99              0.10 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
            110.1             244.5 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
           41.390            41.605 
[1] "25.0 - 110.1 (41.4)" "0.1 - 244.5 (41.6)" 
[1] "hr="     "2.6e+07"
D21V2, continuous
                   vv
clus                IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD11 MUTATED    1       1        2        1        0         0         0
  ANKRD11 WILD-TYPE 45      17       23       10        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ANKRD11 MUTATED           0         0          0          0          0
  ANKRD11 WILD-TYPE         1         2          1          6          5
D21V3, multiclass
            clus
vv           ANKRD11 MUTATED ANKRD11 WILD-TYPE
  IS                       1                45
  STAGE I                  1                17
  STAGE IA                 2                23
  STAGE IB                 1                10
  STAGE II                 0                 4
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
[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                T1 T2 T3
  ANKRD11 MUTATED    3  2  0
  ANKRD11 WILD-TYPE 71 48  6
D21V4, multiclass
    clus
vv   ANKRD11 MUTATED ANKRD11 WILD-TYPE
  T1               3                71
  T2               2                48
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  ANKRD11 MUTATED    2     0
  ANKRD11 WILD-TYPE 43    12
D21V5, multiclass
[1] "Remove cluster labels:" "ANKRD11 MUTATED"       
clus
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                2                55 
       TCGA-2G-AAG0        TCGA-2G-AAEW        TCGA-2G-AAF1        TCGA-2G-AAF4 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFG        TCGA-2G-AAFH 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAFI        TCGA-2G-AAFJ        TCGA-2G-AAFL        TCGA-2G-AAFM 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAG5        TCGA-2G-AAG6        TCGA-2G-AAG7        TCGA-2G-AAG8 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAG9        TCGA-2G-AAGA        TCGA-2G-AAGC        TCGA-2G-AAGE 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAGF        TCGA-2G-AAGG        TCGA-2G-AAGI        TCGA-2G-AAGJ 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN        TCGA-2G-AAGO 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGW        TCGA-2G-AAGX 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH2        TCGA-2G-AAHG 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP        TCGA-2G-AAHT 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7        TCGA-4K-AA1G 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL        TCGA-SO-A8JP 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-VF-A8A8        TCGA-VF-A8AA        TCGA-X3-A8G4 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
D21V6, binary
                   cls
clus                  0   1
  ANKRD11 MUTATED     4   0
  ANKRD11 WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD11 MUTATED      4    0
  ANKRD11 WILD-TYPE  109    4
   clus
vv  ANKRD11 MUTATED ANKRD11 WILD-TYPE
  0               4               109
  1               0                 4
[1] 2 2
[1] FALSE
D21V7, binary
                   cls
clus                  0   1
  ANKRD11 MUTATED     3   2
  ANKRD11 WILD-TYPE 105  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD11 MUTATED      3    2
  ANKRD11 WILD-TYPE  105   19
     clus
vv    ANKRD11 MUTATED ANKRD11 WILD-TYPE
  NO                3               105
  YES               2                19
[1] 2 2
[1] FALSE
D21V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD11 MUTATED       1                         1     3
  ANKRD11 WILD-TYPE     3                         5   113
D21V9, multiclass
                           clus
vv                          ANKRD11 MUTATED ANKRD11 WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   3               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"
D21V10, binary
                   cls
clus                  0   1
  ANKRD11 MUTATED     0   4
  ANKRD11 WILD-TYPE  12 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD11 MUTATED      0    4
  ANKRD11 WILD-TYPE   12  105
                        clus
vv                       ANKRD11 MUTATED ANKRD11 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4               105
[1] 2 2
[1] FALSE

Clustering(22) Variable = ATXN3 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  ATXN3 MUTATED     3   0
  ATXN3 WILD-TYPE 124   4
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             128 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              0               4 
$`ATXN3 MUTATED`
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-XE-AAOC 
      161.06       172.04         8.88 

$`ATXN3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY 
      132.10       158.33       144.85       148.83       181.28       175.20 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  ATXN3 MUTATED ATXN3 WILD-TYPE 
           8.88            0.10 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
         172.04          244.50 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
        161.060          41.455 
[1] "8.9 - 172.0 (161.1)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9200000"
D22V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATXN3 MUTATED    1       0        1        0        0         0         0
  ATXN3 WILD-TYPE 45      18       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ATXN3 MUTATED           0         0          1          0          0
  ATXN3 WILD-TYPE         1         2          0          6          5
D22V3, multiclass
            clus
vv           ATXN3 MUTATED ATXN3 WILD-TYPE
  IS                     1              45
  STAGE I                0              18
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             1               0
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  ATXN3 MUTATED    2  1  0
  ATXN3 WILD-TYPE 72 49  6
D22V4, multiclass
    clus
vv   ATXN3 MUTATED ATXN3 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  ATXN3 MUTATED    1     1
  ATXN3 WILD-TYPE 44    11
D22V5, multiclass
[1] "Remove cluster labels:" "ATXN3 MUTATED"         
clus
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGX 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAH2      TCGA-2G-AAHG      TCGA-2G-AAHL 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKG 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G      TCGA-4K-AA1H 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP      TCGA-VF-A8A8 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
D22V6, binary
                 cls
clus                0   1
  ATXN3 MUTATED     2   1
  ATXN3 WILD-TYPE 111   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      2    1
  ATXN3 WILD-TYPE  111    3
   clus
vv  ATXN3 MUTATED ATXN3 WILD-TYPE
  0             2             111
  1             1               3
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  ATXN3 MUTATED     3   0
  ATXN3 WILD-TYPE 105  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      3    0
  ATXN3 WILD-TYPE  105   21
     clus
vv    ATXN3 MUTATED ATXN3 WILD-TYPE
  NO              3             105
  YES             0              21
[1] 2 2
[1] FALSE
D22V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATXN3 MUTATED       0                         0     3
  ATXN3 WILD-TYPE     4                         6   113
D22V9, multiclass
                           clus
vv                          ATXN3 MUTATED ATXN3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D22V10, binary
                 cls
clus                0   1
  ATXN3 MUTATED     1   2
  ATXN3 WILD-TYPE  11 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      1    2
  ATXN3 WILD-TYPE   11  107
                        clus
vv                       ATXN3 MUTATED ATXN3 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(23) Variable = TPTE2 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED     4   0
  TPTE2 WILD-TYPE 123   4
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             127 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              0               4 
$`TPTE2 MUTATED`
TCGA-2G-AAHA TCGA-SB-A76C TCGA-SO-A8JP TCGA-XE-A8H4 
      110.10         1.38        17.75        18.38 

$`TPTE2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       73.91       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
       13.58        16.31         9.63        10.26        17.23        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           1.38            0.10 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          110.1           244.5 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
         18.065          41.690 
[1] "1.4 - 110.1 (18.1)" "0.1 - 244.5 (41.7)"
[1] "hr="     "9300000"
D23V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPTE2 MUTATED    0       1        1        1        0         0         0
  TPTE2 WILD-TYPE 46      17       24       10        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TPTE2 MUTATED           0         0          0          0          0
  TPTE2 WILD-TYPE         1         2          1          6          5
D23V3, multiclass
            clus
vv           TPTE2 MUTATED TPTE2 WILD-TYPE
  IS                     0              46
  STAGE I                1              17
  STAGE IA               1              24
  STAGE IB               1              10
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  TPTE2 MUTATED    2  1  0
  TPTE2 WILD-TYPE 72 49  6
D23V4, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  TPTE2 MUTATED    1     0
  TPTE2 WILD-TYPE 44    12
D23V5, multiclass
[1] "Remove cluster labels:" "TPTE2 MUTATED"         
clus
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              1              56 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGW 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAHT      TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AA1I      TCGA-4K-AAAL 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-VF-A8A8      TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
D23V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED     4   0
  TPTE2 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      4    0
  TPTE2 WILD-TYPE  109    4
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  TPTE2 MUTATED     3   1
  TPTE2 WILD-TYPE 105  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      3    1
  TPTE2 WILD-TYPE  105   20
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO              3             105
  YES             1              20
[1] 2 2
[1] FALSE
D23V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED       0                         0     4
  TPTE2 WILD-TYPE     4                         6   112
D23V9, multiclass
                           clus
vv                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D23V10, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0   4
  TPTE2 WILD-TYPE  12 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0    4
  TPTE2 WILD-TYPE   12  105
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(24) Variable = KRTAP10-10 MUTATION ANALYSIS
D24V1, survival
                      sevent
clus2                    0   1
  KRTAP10-10 MUTATED     4   0
  KRTAP10-10 WILD-TYPE 123   4
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  127 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   0                    4 
$`KRTAP10-10 MUTATED`
TCGA-ZM-AA0E TCGA-2G-AAEX TCGA-2G-AAH2 TCGA-XE-AAOJ 
       26.66        41.39       199.23        50.96 

$`KRTAP10-10 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 
       50.27        52.37        20.32        46.13        76.11       114.77 
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      128.58       203.28        45.21        22.19        26.04        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        25.41        22.52        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      180.07        59.90       204.16        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        41.69         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
               26.66                 0.10 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
              199.23               244.50 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
              46.175               41.520 
[1] "26.7 - 199.2 (46.2)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "2.6e+07"
D24V2, continuous
                      vv
clus                   IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KRTAP10-10 MUTATED    3       0        1        0        0         0
  KRTAP10-10 WILD-TYPE 43      18       24       11        4         5
                      vv
clus                   STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KRTAP10-10 MUTATED           0         0         0          0          0
  KRTAP10-10 WILD-TYPE         1         1         2          1          6
                      vv
clus                   STAGE IIIC
  KRTAP10-10 MUTATED            0
  KRTAP10-10 WILD-TYPE          5
D24V3, multiclass
            clus
vv           KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  IS                          3                   43
  STAGE I                     0                   18
  STAGE IA                    1                   24
  STAGE IB                    0                   11
  STAGE II                    0                    4
  STAGE IIA                   0                    5
  STAGE IIB                   0                    1
  STAGE IIC                   0                    1
  STAGE III                   0                    2
  STAGE IIIA                  0                    1
  STAGE IIIB                  0                    6
  STAGE IIIC                  0                    5
[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                   T1 T2 T3
  KRTAP10-10 MUTATED    4  0  0
  KRTAP10-10 WILD-TYPE 70 50  6
D24V4, multiclass
    clus
vv   KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  T1                  4                   70
  T2                  0                   50
  T3                  0                    6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   N0 N1+N2
  KRTAP10-10 MUTATED    2     0
  KRTAP10-10 WILD-TYPE 43    12
D24V5, multiclass
[1] "Remove cluster labels:" "KRTAP10-10 MUTATED"    
clus
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   2                   55 
          TCGA-2G-AAG0           TCGA-2G-AAEW           TCGA-2G-AAF1 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAF4           TCGA-2G-AAF6           TCGA-2G-AAF8 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFG           TCGA-2G-AAFH           TCGA-2G-AAFI 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFJ           TCGA-2G-AAFL           TCGA-2G-AAFM 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFN           TCGA-2G-AAFO           TCGA-2G-AAFV 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFY           TCGA-2G-AAG5           TCGA-2G-AAG6 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAG7           TCGA-2G-AAG8           TCGA-2G-AAG9 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGA           TCGA-2G-AAGC           TCGA-2G-AAGE 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGF           TCGA-2G-AAGG           TCGA-2G-AAGI 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGJ           TCGA-2G-AAGK           TCGA-2G-AAGM 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGN           TCGA-2G-AAGO           TCGA-2G-AAGP 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGS           TCGA-2G-AAGW           TCGA-2G-AAGX 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAGY           TCGA-2G-AAGZ           TCGA-2G-AAHG 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAHL           TCGA-2G-AAHN           TCGA-2G-AAHP 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAHT           TCGA-2G-AAKG           TCGA-2G-AAL5 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAL7           TCGA-4K-AA1G           TCGA-4K-AA1H 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-4K-AA1I           TCGA-4K-AAAL           TCGA-SO-A8JP 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-VF-A8A8           TCGA-VF-A8AA           TCGA-VF-A8AB 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-X3-A8G4 
"KRTAP10-10 WILD-TYPE" 
D24V6, binary
                      cls
clus                     0   1
  KRTAP10-10 MUTATED     4   0
  KRTAP10-10 WILD-TYPE 109   4
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-10 MUTATED      4    0
  KRTAP10-10 WILD-TYPE  109    4
   clus
vv  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  0                  4                  109
  1                  0                    4
[1] 2 2
[1] FALSE
D24V7, binary
                      cls
clus                     0   1
  KRTAP10-10 MUTATED     3   1
  KRTAP10-10 WILD-TYPE 105  20
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-10 MUTATED      3    1
  KRTAP10-10 WILD-TYPE  105   20
     clus
vv    KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  NO                   3                  105
  YES                  1                   20
[1] 2 2
[1] FALSE
D24V8, continuous
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-10 MUTATED       0                         0     4
  KRTAP10-10 WILD-TYPE     4                         6   112
D24V9, multiclass
                           clus
vv                          KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  ASIAN                                      0                    4
  BLACK OR AFRICAN AMERICAN                  0                    6
  WHITE                                      4                  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"
D24V10, binary
                      cls
clus                     0   1
  KRTAP10-10 MUTATED     1   3
  KRTAP10-10 WILD-TYPE  11 106
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-10 MUTATED      1    3
  KRTAP10-10 WILD-TYPE   11  106
                        clus
vv                       KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  HISPANIC OR LATINO                      1                   11
  NOT HISPANIC OR LATINO                  3                  106
[1] 2 2
[1] FALSE

Clustering(25) Variable = ZNF680 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  ZNF680 MUTATED     3   0
  ZNF680 WILD-TYPE 124   4
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               3              128 
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               0                4 
$`ZNF680 MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAH8 TCGA-VF-A8AA 
      114.77        73.91        37.68 

$`ZNF680 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
       76.11       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA 
      172.04       180.07       199.23        59.90       204.16       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  ZNF680 MUTATED ZNF680 WILD-TYPE 
           37.68             0.10 
  ZNF680 MUTATED ZNF680 WILD-TYPE 
          114.77           244.50 
  ZNF680 MUTATED ZNF680 WILD-TYPE 
          73.910           41.455 
[1] "37.7 - 114.8 (73.9)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9300000"
D25V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF680 MUTATED    1       1        0        0        0         0         0
  ZNF680 WILD-TYPE 45      17       25       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZNF680 MUTATED           0         0          0          0          1
  ZNF680 WILD-TYPE         1         2          1          6          4
D25V3, multiclass
            clus
vv           ZNF680 MUTATED ZNF680 WILD-TYPE
  IS                      1               45
  STAGE I                 1               17
  STAGE IA                0               25
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              1                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               T1 T2 T3
  ZNF680 MUTATED    2  1  0
  ZNF680 WILD-TYPE 72 49  6
D25V4, multiclass
    clus
vv   ZNF680 MUTATED ZNF680 WILD-TYPE
  T1              2               72
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  ZNF680 MUTATED    2     0
  ZNF680 WILD-TYPE 43    12
D25V5, multiclass
[1] "Remove cluster labels:" "ZNF680 MUTATED"        
clus
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               2               55 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AB       TCGA-X3-A8G4 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
D25V6, binary
                  cls
clus                 0   1
  ZNF680 MUTATED     3   0
  ZNF680 WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF680 MUTATED      3    0
  ZNF680 WILD-TYPE  110    4
   clus
vv  ZNF680 MUTATED ZNF680 WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D25V7, binary
                  cls
clus                 0   1
  ZNF680 MUTATED     2   1
  ZNF680 WILD-TYPE 106  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF680 MUTATED      2    1
  ZNF680 WILD-TYPE  106   20
     clus
vv    ZNF680 MUTATED ZNF680 WILD-TYPE
  NO               2              106
  YES              1               20
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "ZNF680 MUTATED"        
clus
  ZNF680 MUTATED ZNF680 WILD-TYPE 
               2               99 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEX 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF8       TCGA-2G-AAFG 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5       TCGA-2G-AAG6 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK       TCGA-2G-AAGM 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP       TCGA-2G-AAGS 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW       TCGA-2G-AAGX 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0       TCGA-2G-AAH2 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAHA       TCGA-2G-AAHC 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG       TCGA-2G-AAKH 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5       TCGA-2G-AAL7 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6       TCGA-4K-AA1G 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AAAL       TCGA-S6-A8JW       TCGA-S6-A8JX 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-SB-A6J6       TCGA-SB-A76C       TCGA-SN-A84Y       TCGA-SO-A8JP 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5       TCGA-WZ-A8D5 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5       TCGA-XE-A9SE 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR       TCGA-XE-AANV 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6       TCGA-XE-AAOC 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ       TCGA-XE-AAOL 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B       TCGA-ZM-AA0D 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
      TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" "ZNF680 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF680 MUTATED       0                         0     3
  ZNF680 WILD-TYPE     4                         6   113
D25V9, multiclass
                           clus
vv                          ZNF680 MUTATED ZNF680 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D25V10, binary
                  cls
clus                 0   1
  ZNF680 MUTATED     0   3
  ZNF680 WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF680 MUTATED      0    3
  ZNF680 WILD-TYPE   12  106
                        clus
vv                       ZNF680 MUTATED ZNF680 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(26) Variable = RAC1 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     4   0
  RAC1 WILD-TYPE 123   4
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            127 
  RAC1 MUTATED RAC1 WILD-TYPE 
             0              4 
$`RAC1 MUTATED`
TCGA-2G-AAHT TCGA-2G-AAL7 TCGA-4K-AAAL TCGA-XE-AANV 
       17.82       131.21        15.88        55.92 

$`RAC1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      186.31       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      244.50        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
        0.46        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  RAC1 MUTATED RAC1 WILD-TYPE 
         15.88           0.10 
  RAC1 MUTATED RAC1 WILD-TYPE 
        131.21         244.50 
  RAC1 MUTATED RAC1 WILD-TYPE 
         36.87          41.52 
[1] "15.9 - 131.2 (36.9)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9300000"
D26V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAC1 MUTATED    3       0        0        1        0         0         0
  RAC1 WILD-TYPE 43      18       25       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RAC1 MUTATED           0         0          0          0          0
  RAC1 WILD-TYPE         1         2          1          6          5
D26V3, multiclass
            clus
vv           RAC1 MUTATED RAC1 WILD-TYPE
  IS                    3             43
  STAGE I               0             18
  STAGE IA              0             25
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  RAC1 MUTATED    0  4  0
  RAC1 WILD-TYPE 74 46  6
D26V4, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  T1            0             74
  T2            4             46
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  RAC1 MUTATED    3     0
  RAC1 WILD-TYPE 42    12
D26V5, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  N0               3             42
  N1+N2            0             12
[1] 2 2
[1] FALSE
D26V6, binary
                cls
clus               0   1
  RAC1 MUTATED     4   0
  RAC1 WILD-TYPE 109   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    0
  RAC1 WILD-TYPE  109    4
   clus
vv  RAC1 MUTATED RAC1 WILD-TYPE
  0            4            109
  1            0              4
[1] 2 2
[1] FALSE
D26V7, binary
                cls
clus               0   1
  RAC1 MUTATED     3   1
  RAC1 WILD-TYPE 105  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      3    1
  RAC1 WILD-TYPE  105   20
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  NO             3            105
  YES            1             20
[1] 2 2
[1] FALSE
D26V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED       0                         0     3
  RAC1 WILD-TYPE     4                         6   113
D26V9, multiclass
                           clus
vv                          RAC1 MUTATED RAC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            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"
D26V10, binary
                cls
clus               0   1
  RAC1 MUTATED     0   4
  RAC1 WILD-TYPE  12 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0    4
  RAC1 WILD-TYPE   12  105
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            4            105
[1] 2 2
[1] FALSE

Clustering(27) Variable = NBPF10 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  NBPF10 MUTATED     6   1
  NBPF10 WILD-TYPE 121   3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               7              124 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               1                3 
$`NBPF10 MUTATED`
TCGA-2G-AAFL TCGA-2G-AAFO TCGA-2G-AAHA TCGA-XE-AAOB TCGA-XE-AAOL TCGA-YU-A90P 
       24.66        22.52       110.10        16.87         0.43        68.02 
TCGA-YU-A94D 
       71.24 

$`NBPF10 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       26.04        16.54        25.41        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC 
      180.07       199.23        59.90       204.16        73.91       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOC 
        0.46        55.92        93.93        12.07         7.89         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69        50.96        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
        9.24        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
       17.62        51.72        28.41        37.02        49.25        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.88        22.39        57.07        20.84 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            0.43             0.10 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           110.1            244.5 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
          24.660           41.605 
[1] "0.4 - 110.1 (24.7)" "0.1 - 244.5 (41.6)"
[1] "hr=" "9.5"
D27V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NBPF10 MUTATED    1       1        1        2        0         1         0
  NBPF10 WILD-TYPE 45      17       24        9        4         4         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NBPF10 MUTATED           0         0          0          1          0
  NBPF10 WILD-TYPE         1         2          1          5          5
D27V3, multiclass
            clus
vv           NBPF10 MUTATED NBPF10 WILD-TYPE
  IS                      1               45
  STAGE I                 1               17
  STAGE IA                1               24
  STAGE IB                2                9
  STAGE II                0                4
  STAGE IIA               1                4
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              1                5
  STAGE IIIC              0                5
[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               T1 T2 T3
  NBPF10 MUTATED    4  2  1
  NBPF10 WILD-TYPE 70 48  5
D27V4, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  T1              4               70
  T2              2               48
  T3              1                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  NBPF10 MUTATED    1     1
  NBPF10 WILD-TYPE 44    11
D27V5, multiclass
[1] "Remove cluster labels:" "NBPF10 MUTATED"        
clus
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               2               55 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFM 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAG5 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX       TCGA-2G-AAGY 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG       TCGA-2G-AAHL 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKG 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G       TCGA-4K-AA1H 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP       TCGA-VF-A8A8 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
D27V6, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     5   0
  NBPF10 WILD-TYPE 108   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      5    0
  NBPF10 WILD-TYPE  108    4
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              5              108
  1              0                4
[1] 2 2
[1] FALSE
D27V7, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     6   0
  NBPF10 WILD-TYPE 102  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      6    0
  NBPF10 WILD-TYPE  102   21
     clus
vv    NBPF10 MUTATED NBPF10 WILD-TYPE
  NO               6              102
  YES              0               21
[1] 2 2
[1] FALSE
D27V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED       0                         1     5
  NBPF10 WILD-TYPE     4                         5   111
D27V9, multiclass
                           clus
vv                          NBPF10 MUTATED NBPF10 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                  5              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"
D27V10, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     0   5
  NBPF10 WILD-TYPE  12 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      0    5
  NBPF10 WILD-TYPE   12  104
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              5              104
[1] 2 2
[1] FALSE

Clustering(28) Variable = FAM8A1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  FAM8A1 MUTATED     3   0
  FAM8A1 WILD-TYPE 124   4
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              128 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               0                4 
$`FAM8A1 MUTATED`
TCGA-2G-AAHA TCGA-4K-AAAL TCGA-XE-A8H4 
      110.10        15.88        18.38 

$`FAM8A1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       73.91       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
       17.03         0.10        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           15.88             0.10 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           110.1            244.5 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
          18.380           41.605 
[1] "15.9 - 110.1 (18.4)" "0.1 - 244.5 (41.6)" 
[1] "hr="     "9200000"
D28V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM8A1 MUTATED    1       0        1        1        0         0         0
  FAM8A1 WILD-TYPE 45      18       24       10        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM8A1 MUTATED           0         0          0          0          0
  FAM8A1 WILD-TYPE         1         2          1          6          5
D28V3, multiclass
            clus
vv           FAM8A1 MUTATED FAM8A1 WILD-TYPE
  IS                      1               45
  STAGE I                 0               18
  STAGE IA                1               24
  STAGE IB                1               10
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  FAM8A1 MUTATED    0  2  0
  FAM8A1 WILD-TYPE 74 48  6
D28V4, multiclass
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2              128 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEW 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGT       TCGA-2G-AAGV 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGW       TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAH0       TCGA-2G-AAH2       TCGA-2G-AAH3       TCGA-2G-AAH4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAH8       TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2X-A9D6       TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AA1I 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-S6-A8JW       TCGA-S6-A8JX       TCGA-S6-A8JY       TCGA-SB-A6J6 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-SB-A76C       TCGA-SN-A6IS       TCGA-SN-A84W       TCGA-SN-A84X 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-SN-A84Y       TCGA-SO-A8JP       TCGA-VF-A8A8       TCGA-VF-A8AA 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-VF-A8AB       TCGA-VF-A8AC       TCGA-VF-A8AD       TCGA-VF-A8AE 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-W4-A7U2       TCGA-W4-A7U4       TCGA-WZ-A7V3       TCGA-WZ-A7V4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-WZ-A7V5       TCGA-WZ-A8D5       TCGA-X3-A8G4       TCGA-XE-A8H1 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-A8H5       TCGA-XE-A9SE       TCGA-XE-AANI       TCGA-XE-AANJ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AANR       TCGA-XE-AANV       TCGA-XE-AAO3       TCGA-XE-AAO4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AAO6       TCGA-XE-AAOB       TCGA-XE-AAOC       TCGA-XE-AAOD 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AAOF       TCGA-XE-AAOJ       TCGA-XE-AAOL       TCGA-XY-A89B 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XY-A8S2       TCGA-XY-A8S3       TCGA-XY-A9T9       TCGA-YU-A90P 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YU-A90Q       TCGA-YU-A90S       TCGA-YU-A90W       TCGA-YU-A90Y 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YU-A912       TCGA-YU-A94D       TCGA-YU-A94I       TCGA-YU-AA4L 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YU-AA61       TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-ZM-AA0D       TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
                  vv
clus               N0 N1+N2
  FAM8A1 MUTATED    1     0
  FAM8A1 WILD-TYPE 44    12
D28V5, multiclass
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               1               56 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFY       TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGJ       TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGO       TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAHT       TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-SO-A8JP 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
D28V6, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     3   0
  FAM8A1 WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      3    0
  FAM8A1 WILD-TYPE  110    4
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     2   1
  FAM8A1 WILD-TYPE 106  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    1
  FAM8A1 WILD-TYPE  106   20
     clus
vv    FAM8A1 MUTATED FAM8A1 WILD-TYPE
  NO               2              106
  YES              1               20
[1] 2 2
[1] FALSE
D28V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM8A1 MUTATED       0                         0     3
  FAM8A1 WILD-TYPE     4                         6   113
D28V9, multiclass
                           clus
vv                          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D28V10, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     0   3
  FAM8A1 WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      0    3
  FAM8A1 WILD-TYPE   12  106
                        clus
vv                       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(29) Variable = PSMD11 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  PSMD11 MUTATED     4   0
  PSMD11 WILD-TYPE 123   4
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              127 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               0                4 
$`PSMD11 MUTATED`
TCGA-2G-AAEX TCGA-WZ-A7V5 TCGA-XE-AAO6 TCGA-XY-A89B 
       41.39        34.88         7.89        15.48 

$`PSMD11 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        20.32        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.75        37.18        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 
       23.90        41.52        24.26        24.76        29.39        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB 
       65.98         0.46        55.92        93.93        12.07        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 
        8.88        67.66        41.69        50.96         0.43        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  PSMD11 MUTATED PSMD11 WILD-TYPE 
            7.89             0.10 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           41.39           244.50 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           25.18            44.48 
[1] "7.9 - 41.4 (25.2)"  "0.1 - 244.5 (44.5)"
[1] "hr="     "9200000"
D29V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSMD11 MUTATED    1       1        2        0        0         0         0
  PSMD11 WILD-TYPE 45      17       23       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PSMD11 MUTATED           0         0          0          0          0
  PSMD11 WILD-TYPE         1         2          1          6          5
D29V3, multiclass
            clus
vv           PSMD11 MUTATED PSMD11 WILD-TYPE
  IS                      1               45
  STAGE I                 1               17
  STAGE IA                2               23
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  PSMD11 MUTATED    3  1  0
  PSMD11 WILD-TYPE 71 49  6
D29V4, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  T1              3               71
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PSMD11 MUTATED    1     0
  PSMD11 WILD-TYPE 44    12
D29V5, multiclass
[1] "Remove cluster labels:" "PSMD11 MUTATED"        
clus
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               1               56 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAF1       TCGA-2G-AAF4 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
D29V6, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     3   0
  PSMD11 WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      3    0
  PSMD11 WILD-TYPE  110    4
   clus
vv  PSMD11 MUTATED PSMD11 WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     1   3
  PSMD11 WILD-TYPE 107  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      1    3
  PSMD11 WILD-TYPE  107   18
     clus
vv    PSMD11 MUTATED PSMD11 WILD-TYPE
  NO               1              107
  YES              3               18
[1] 2 2
[1] FALSE
D29V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSMD11 MUTATED       0                         0     4
  PSMD11 WILD-TYPE     4                         6   112
D29V9, multiclass
                           clus
vv                          PSMD11 MUTATED PSMD11 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D29V10, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     0   4
  PSMD11 WILD-TYPE  12 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      0    4
  PSMD11 WILD-TYPE   12  105
                        clus
vv                       PSMD11 MUTATED PSMD11 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4              105
[1] 2 2
[1] FALSE

Clustering(30) Variable = KRTAP1-1 MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  KRTAP1-1 MUTATED     3   0
  KRTAP1-1 WILD-TYPE 124   4
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                128 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 0                  4 
$`KRTAP1-1 MUTATED`
TCGA-2G-AAFI TCGA-WZ-A8D5 TCGA-XE-AAOF 
       22.19        25.45        41.69 

$`KRTAP1-1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ 
       76.11       114.77       128.58       203.28        45.21        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.75        37.18        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52        24.26        24.76        29.39        34.88 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
       16.87         8.88        67.66        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             22.19               0.10 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             41.69             244.50 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             25.45              43.00 
[1] "22.2 - 41.7 (25.4)" "0.1 - 244.5 (43.0)"
[1] "hr="     "9300000"
D30V2, continuous
                    vv
clus                 IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP1-1 MUTATED    0       0        1        1        0         0         0
  KRTAP1-1 WILD-TYPE 46      18       24       10        4         5         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRTAP1-1 MUTATED           0         0          0          0          0
  KRTAP1-1 WILD-TYPE         1         2          1          6          5
D30V3, multiclass
[1] "Remove cluster labels:" "KRTAP1-1 MUTATED"      
clus
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 2                123 
        TCGA-2G-AAG0         TCGA-2G-AAG3         TCGA-ZM-AA0E 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAEW         TCGA-2G-AAEX         TCGA-2G-AAF1 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAF4         TCGA-2G-AAF6         TCGA-2G-AAF8 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFG         TCGA-2G-AAFH         TCGA-2G-AAFL 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFM         TCGA-2G-AAFN         TCGA-2G-AAFO 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFV         TCGA-2G-AAFY         TCGA-2G-AAFZ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAG5         TCGA-2G-AAG6         TCGA-2G-AAG7 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAG8         TCGA-2G-AAG9         TCGA-2G-AAGA 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGC         TCGA-2G-AAGE         TCGA-2G-AAGF 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGG         TCGA-2G-AAGI         TCGA-2G-AAGJ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGK         TCGA-2G-AAGM         TCGA-2G-AAGN 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGO         TCGA-2G-AAGP         TCGA-2G-AAGS 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGT         TCGA-2G-AAGW         TCGA-2G-AAGX 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGY         TCGA-2G-AAGZ         TCGA-2G-AAH0 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAH2         TCGA-2G-AAH3         TCGA-2G-AAH4 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAH8         TCGA-2G-AAHA         TCGA-2G-AAHC 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHG         TCGA-2G-AAHL         TCGA-2G-AAHN 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHP         TCGA-2G-AAHT         TCGA-2G-AAKD 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAKG         TCGA-2G-AAKH         TCGA-2G-AAKL 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAKM         TCGA-2G-AAL5         TCGA-2G-AAL7 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AALP         TCGA-2X-A9D5         TCGA-2X-A9D6 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-4K-AA1G         TCGA-4K-AA1H         TCGA-4K-AA1I 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-4K-AAAL         TCGA-S6-A8JW         TCGA-S6-A8JX 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-S6-A8JY         TCGA-SB-A6J6         TCGA-SN-A6IS 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-SN-A84W         TCGA-SN-A84X         TCGA-SN-A84Y 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-SO-A8JP         TCGA-VF-A8A8         TCGA-VF-A8AA 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VF-A8AB         TCGA-VF-A8AC         TCGA-VF-A8AD 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VF-A8AE         TCGA-WZ-A7V3         TCGA-WZ-A7V4 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-WZ-A7V5         TCGA-X3-A8G4         TCGA-XE-A8H1 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-A8H4         TCGA-XE-A8H5         TCGA-XE-A9SE 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-AANI         TCGA-XE-AANJ         TCGA-XE-AANR 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-AANV         TCGA-XE-AAO3         TCGA-XE-AAO4 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-AAO6         TCGA-XE-AAOB         TCGA-XE-AAOC 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-AAOD         TCGA-XE-AAOJ         TCGA-XE-AAOL 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XY-A89B         TCGA-XY-A8S2         TCGA-XY-A8S3 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XY-A9T9         TCGA-YU-A90P         TCGA-YU-A90Q 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-YU-A90S         TCGA-YU-A90W         TCGA-YU-A90Y 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-YU-A912         TCGA-YU-A94D         TCGA-YU-A94I 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-YU-AA4L         TCGA-YU-AA61         TCGA-ZM-AA05 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-ZM-AA06         TCGA-ZM-AA0B         TCGA-ZM-AA0D 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-ZM-AA0F         TCGA-ZM-AA0H         TCGA-ZM-AA0N 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
                    vv
clus                 T1 T2 T3
  KRTAP1-1 MUTATED    1  1  1
  KRTAP1-1 WILD-TYPE 73 49  5
D30V4, multiclass
    clus
vv   KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  T1                1                 73
  T2                1                 49
  T3                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1+N2
  KRTAP1-1 MUTATED    1     0
  KRTAP1-1 WILD-TYPE 44    12
D30V5, multiclass
[1] "Remove cluster labels:" "KRTAP1-1 MUTATED"      
clus
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 1                 56 
        TCGA-2G-AAG0         TCGA-2G-AAEW         TCGA-2G-AAEX 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAF1         TCGA-2G-AAF4         TCGA-2G-AAF6 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAF8         TCGA-2G-AAFG         TCGA-2G-AAFH 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFJ         TCGA-2G-AAFL         TCGA-2G-AAFM 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFN         TCGA-2G-AAFO         TCGA-2G-AAFV 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFY         TCGA-2G-AAG5         TCGA-2G-AAG6 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAG7         TCGA-2G-AAG8         TCGA-2G-AAG9 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGA         TCGA-2G-AAGC         TCGA-2G-AAGE 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGF         TCGA-2G-AAGG         TCGA-2G-AAGI 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGJ         TCGA-2G-AAGK         TCGA-2G-AAGM 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGN         TCGA-2G-AAGO         TCGA-2G-AAGP 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGS         TCGA-2G-AAGW         TCGA-2G-AAGX 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGY         TCGA-2G-AAGZ         TCGA-2G-AAH2 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHG         TCGA-2G-AAHL         TCGA-2G-AAHN 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHP         TCGA-2G-AAHT         TCGA-2G-AAKG 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAL5         TCGA-2G-AAL7         TCGA-4K-AA1G 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-4K-AA1H         TCGA-4K-AA1I         TCGA-4K-AAAL 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-SO-A8JP         TCGA-VF-A8A8         TCGA-VF-A8AA 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VF-A8AB         TCGA-X3-A8G4 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
D30V6, binary
                    cls
clus                   0   1
  KRTAP1-1 MUTATED     3   0
  KRTAP1-1 WILD-TYPE 110   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      3    0
  KRTAP1-1 WILD-TYPE  110    4
   clus
vv  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  0                3                110
  1                0                  4
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  KRTAP1-1 MUTATED     1   2
  KRTAP1-1 WILD-TYPE 107  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      1    2
  KRTAP1-1 WILD-TYPE  107   19
     clus
vv    KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  NO                 1                107
  YES                2                 19
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP1-1 MUTATED       1                         0     2
  KRTAP1-1 WILD-TYPE     3                         6   114
D30V9, multiclass
                           clus
vv                          KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    2                114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                    cls
clus                   0   1
  KRTAP1-1 MUTATED     0   3
  KRTAP1-1 WILD-TYPE  12 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      0    3
  KRTAP1-1 WILD-TYPE   12  106
                        clus
vv                       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                106
[1] 2 2
[1] FALSE

Clustering(31) Variable = OPLAH MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  OPLAH MUTATED     4   0
  OPLAH WILD-TYPE 123   4
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             127 
  OPLAH MUTATED OPLAH WILD-TYPE 
              0               4 
$`OPLAH MUTATED`
TCGA-2G-AAGS TCGA-2G-AAGZ TCGA-2X-A9D6 TCGA-SB-A6J6 
      158.33       172.04        19.96        13.58 

$`OPLAH WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      132.10       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        86.96        14.30        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS 
       15.88        22.95        18.15         9.14         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  OPLAH MUTATED OPLAH WILD-TYPE 
          13.58            0.10 
  OPLAH MUTATED OPLAH WILD-TYPE 
         172.04          244.50 
  OPLAH MUTATED OPLAH WILD-TYPE 
         89.145          41.520 
[1] "13.6 - 172.0 (89.1)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9300000"
D31V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPLAH MUTATED    0       1        1        0        0         0         0
  OPLAH WILD-TYPE 46      17       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OPLAH MUTATED           0         0          1          1          0
  OPLAH WILD-TYPE         1         2          0          5          5
D31V3, multiclass
            clus
vv           OPLAH MUTATED OPLAH WILD-TYPE
  IS                     0              46
  STAGE I                1              17
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             1               0
  STAGE IIIB             1               5
  STAGE IIIC             0               5
[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              T1 T2 T3
  OPLAH MUTATED    3  1  0
  OPLAH WILD-TYPE 71 49  6
D31V4, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  T1             3              71
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  OPLAH MUTATED    0     2
  OPLAH WILD-TYPE 45    10
D31V5, multiclass
[1] "Remove cluster labels:" "OPLAH MUTATED"         
clus
  OPLAH MUTATED OPLAH WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGW      TCGA-2G-AAGX 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAH2      TCGA-2G-AAHG      TCGA-2G-AAHL 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKG 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G      TCGA-4K-AA1H 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP      TCGA-VF-A8A8 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
D31V6, binary
                 cls
clus                0   1
  OPLAH MUTATED     3   1
  OPLAH WILD-TYPE 110   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      3    1
  OPLAH WILD-TYPE  110    3
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0             3             110
  1             1               3
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus                0   1
  OPLAH MUTATED     4   0
  OPLAH WILD-TYPE 104  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      4    0
  OPLAH WILD-TYPE  104   21
     clus
vv    OPLAH MUTATED OPLAH WILD-TYPE
  NO              4             104
  YES             0              21
[1] 2 2
[1] FALSE
D31V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OPLAH MUTATED       0                         0     4
  OPLAH WILD-TYPE     4                         6   112
D31V9, multiclass
                           clus
vv                          OPLAH MUTATED OPLAH WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D31V10, binary
                 cls
clus                0   1
  OPLAH MUTATED     0   4
  OPLAH WILD-TYPE  12 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      0    4
  OPLAH WILD-TYPE   12  105
                        clus
vv                       OPLAH MUTATED OPLAH WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(32) Variable = FAM101B MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  FAM101B MUTATED     4   0
  FAM101B WILD-TYPE 123   4
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               127 
  FAM101B MUTATED FAM101B WILD-TYPE 
                0                 4 
$`FAM101B MUTATED`
TCGA-2G-AAFJ TCGA-SN-A84Y TCGA-VF-A8AE TCGA-XE-AAOL 
       26.04        17.23        23.90         0.43 

$`FAM101B WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP 
       13.58         1.38        16.31         9.63        10.26        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
       37.18        37.68        24.99        35.61        33.07        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        41.69        50.96        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  FAM101B MUTATED FAM101B WILD-TYPE 
             0.43              0.10 
  FAM101B MUTATED FAM101B WILD-TYPE 
            26.04            244.50 
  FAM101B MUTATED FAM101B WILD-TYPE 
           20.565            44.480 
[1] "0.4 - 26.0 (20.6)"  "0.1 - 244.5 (44.5)"
[1] "hr="     "9200000"
D32V2, continuous
                   vv
clus                IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM101B MUTATED    1       1        1        0        0         0         0
  FAM101B WILD-TYPE 45      17       24       11        4         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM101B MUTATED           0         0          0          0          0
  FAM101B WILD-TYPE         1         2          1          6          5
D32V3, multiclass
            clus
vv           FAM101B MUTATED FAM101B WILD-TYPE
  IS                       1                45
  STAGE I                  1                17
  STAGE IA                 1                24
  STAGE IB                 0                11
  STAGE II                 0                 4
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                0                 1
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               0                 5
[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                T1 T2 T3
  FAM101B MUTATED    3  1  0
  FAM101B WILD-TYPE 71 49  6
D32V4, multiclass
    clus
vv   FAM101B MUTATED FAM101B WILD-TYPE
  T1               3                71
  T2               1                49
  T3               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1+N2
  FAM101B MUTATED    1     0
  FAM101B WILD-TYPE 44    12
D32V5, multiclass
[1] "Remove cluster labels:" "FAM101B MUTATED"       
clus
  FAM101B MUTATED FAM101B WILD-TYPE 
                1                56 
       TCGA-2G-AAG0        TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAF4        TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFG 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAFH        TCGA-2G-AAFI        TCGA-2G-AAFL        TCGA-2G-AAFM 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAFN        TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAG5        TCGA-2G-AAG6        TCGA-2G-AAG7        TCGA-2G-AAG8 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAG9        TCGA-2G-AAGA        TCGA-2G-AAGC        TCGA-2G-AAGE 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAGF        TCGA-2G-AAGG        TCGA-2G-AAGI        TCGA-2G-AAGJ 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAGK        TCGA-2G-AAGM        TCGA-2G-AAGN        TCGA-2G-AAGO 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAGP        TCGA-2G-AAGS        TCGA-2G-AAGW        TCGA-2G-AAGX 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAGY        TCGA-2G-AAGZ        TCGA-2G-AAH2        TCGA-2G-AAHG 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAHL        TCGA-2G-AAHN        TCGA-2G-AAHP        TCGA-2G-AAHT 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAKG        TCGA-2G-AAL5        TCGA-2G-AAL7        TCGA-4K-AA1G 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-4K-AA1H        TCGA-4K-AA1I        TCGA-4K-AAAL        TCGA-SO-A8JP 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-VF-A8A8        TCGA-VF-A8AA        TCGA-VF-A8AB        TCGA-X3-A8G4 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
D32V6, binary
                   cls
clus                  0   1
  FAM101B MUTATED     4   0
  FAM101B WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM101B MUTATED      4    0
  FAM101B WILD-TYPE  109    4
   clus
vv  FAM101B MUTATED FAM101B WILD-TYPE
  0               4               109
  1               0                 4
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                  0   1
  FAM101B MUTATED     3   0
  FAM101B WILD-TYPE 105  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM101B MUTATED      3    0
  FAM101B WILD-TYPE  105   21
     clus
vv    FAM101B MUTATED FAM101B WILD-TYPE
  NO                3               105
  YES               0                21
[1] 2 2
[1] FALSE
D32V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM101B MUTATED       1                         1     2
  FAM101B WILD-TYPE     3                         5   114
D32V9, multiclass
                           clus
vv                          FAM101B MUTATED FAM101B WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   2               114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                   cls
clus                  0   1
  FAM101B MUTATED     1   3
  FAM101B WILD-TYPE  11 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM101B MUTATED      1    3
  FAM101B WILD-TYPE   11  106
                        clus
vv                       FAM101B MUTATED FAM101B WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3               106
[1] 2 2
[1] FALSE

Clustering(33) Variable = MUC2 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  MUC2 MUTATED    14   0
  MUC2 WILD-TYPE 113   4
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            117 
  MUC2 MUTATED MUC2 WILD-TYPE 
             0              4 
$`MUC2 MUTATED`
TCGA-2G-AAG0 TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAGA TCGA-2G-AAGS TCGA-2G-AAGX 
       50.27        41.39        76.11        80.19       158.33       181.28 
TCGA-2G-AAH4 TCGA-2G-AAHN TCGA-2G-AAKD TCGA-SO-A8JP TCGA-VF-A8AB TCGA-XE-A8H4 
      204.16       211.89       208.44        17.75        24.99        18.38 
TCGA-XE-AANR TCGA-YU-A94I 
        0.46        17.62 

$`MUC2 WILD-TYPE`
TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 
       52.37        26.66        20.32        46.13       114.77       128.58 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      203.28        45.21        22.19        26.04        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 
       25.41        22.52        45.67        36.13        44.48        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE 
       73.35        81.37        75.25        73.45        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       89.88        85.84       103.13        96.59       119.05       127.92 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW 
      120.20       132.36       132.10       144.85       148.83       161.06 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 
      175.20       172.04       180.07       199.23        59.90        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT 
      110.10       182.10        59.80       232.80       186.31        17.82 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA 
       16.31         9.63        10.26        17.23        37.18        37.68 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 
       29.39        34.88        25.45        28.14         6.87        40.01 
TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       23.28        34.22        65.98        55.92        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ 
        7.89        16.87         8.88        67.66        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43        15.48        22.09        27.72         9.24        68.02 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       64.57        31.92        36.59         0.56        28.47        71.24 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       51.72        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

  MUC2 MUTATED MUC2 WILD-TYPE 
          0.46           0.10 
  MUC2 MUTATED MUC2 WILD-TYPE 
        211.89         244.50 
  MUC2 MUTATED MUC2 WILD-TYPE 
         63.19          40.01 
[1] "0.5 - 211.9 (63.2)" "0.1 - 244.5 (40.0)"
[1] "hr="     "7.9e+07"
D33V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC2 MUTATED    2       4        4        0        1         1         0
  MUC2 WILD-TYPE 44      14       21       11        3         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC2 MUTATED           0         1          0          1          0
  MUC2 WILD-TYPE         1         1          1          5          5
D33V3, multiclass
            clus
vv           MUC2 MUTATED MUC2 WILD-TYPE
  IS                    2             44
  STAGE I               4             14
  STAGE IA              4             21
  STAGE IB              0             11
  STAGE II              1              3
  STAGE IIA             1              4
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             1              1
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            0              5
[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             T1 T2 T3
  MUC2 MUTATED   10  3  0
  MUC2 WILD-TYPE 64 47  6
D33V4, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  T1           10             64
  T2            3             47
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  MUC2 MUTATED    7     2
  MUC2 WILD-TYPE 38    10
D33V5, multiclass
       clus
vv      MUC2 MUTATED MUC2 WILD-TYPE
  N0               7             38
  N1+N2            2             10
[1] 2 2
[1] FALSE
D33V6, binary
                cls
clus               0   1
  MUC2 MUTATED    13   0
  MUC2 WILD-TYPE 100   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     13    0
  MUC2 WILD-TYPE  100    4
   clus
vv  MUC2 MUTATED MUC2 WILD-TYPE
  0           13            100
  1            0              4
[1] 2 2
[1] FALSE
D33V7, binary
                cls
clus              0  1
  MUC2 MUTATED    9  4
  MUC2 WILD-TYPE 99 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      9    4
  MUC2 WILD-TYPE   99   17
     clus
vv    MUC2 MUTATED MUC2 WILD-TYPE
  NO             9             99
  YES            4             17
[1] 2 2
[1] FALSE
D33V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC2 MUTATED       0                         1    12
  MUC2 WILD-TYPE     4                         5   104
D33V9, multiclass
                           clus
vv                          MUC2 MUTATED MUC2 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                               12            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"
D33V10, binary
                cls
clus              0  1
  MUC2 MUTATED    1 12
  MUC2 WILD-TYPE 11 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      1   12
  MUC2 WILD-TYPE   11   97
                        clus
vv                       MUC2 MUTATED MUC2 WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO           12             97
[1] 2 2
[1] FALSE

Clustering(34) Variable = HTT MUTATION ANALYSIS
D34V1, survival
               sevent
clus2             0   1
  HTT MUTATED     3   0
  HTT WILD-TYPE 124   4
  HTT MUTATED HTT WILD-TYPE 
            3           128 
  HTT MUTATED HTT WILD-TYPE 
            0             4 
$`HTT MUTATED`
TCGA-2G-AAFI TCGA-SN-A6IS TCGA-ZM-AA0H 
       22.19        16.31        57.07 

$`HTT WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ 
       76.11       114.77       128.58       203.28        45.21        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58         1.38         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        36.59         0.56        28.47        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       51.72        28.41        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0F TCGA-ZM-AA0N 
       22.39        20.84 

  HTT MUTATED HTT WILD-TYPE 
        16.31          0.10 
  HTT MUTATED HTT WILD-TYPE 
        57.07        244.50 
  HTT MUTATED HTT WILD-TYPE 
       22.190        41.605 
[1] "16.3 - 57.1 (22.2)" "0.1 - 244.5 (41.6)"
[1] "hr="     "9200000"
D34V2, continuous
               vv
clus            IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTT MUTATED    2       0        0        1        0         0         0
  HTT WILD-TYPE 44      18       25       10        4         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HTT MUTATED           0         0          0          0          0
  HTT WILD-TYPE         1         2          1          6          5
D34V3, multiclass
            clus
vv           HTT MUTATED HTT WILD-TYPE
  IS                   2            44
  STAGE I              0            18
  STAGE IA             0            25
  STAGE IB             1            10
  STAGE II             0             4
  STAGE IIA            0             5
  STAGE IIB            0             1
  STAGE IIC            0             1
  STAGE III            0             2
  STAGE IIIA           0             1
  STAGE IIIB           0             6
  STAGE IIIC           0             5
[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            T1 T2 T3
  HTT MUTATED    1  1  1
  HTT WILD-TYPE 73 49  5
D34V4, multiclass
    clus
vv   HTT MUTATED HTT WILD-TYPE
  T1           1            73
  T2           1            49
  T3           1             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  HTT MUTATED    1     0
  HTT WILD-TYPE 44    12
D34V5, multiclass
[1] "Remove cluster labels:" "HTT MUTATED"           
clus
  HTT MUTATED HTT WILD-TYPE 
            1            56 
   TCGA-2G-AAG0    TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAF6    TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFJ 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAFY    TCGA-2G-AAG5    TCGA-2G-AAG6    TCGA-2G-AAG7    TCGA-2G-AAG8 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAG9    TCGA-2G-AAGA    TCGA-2G-AAGC    TCGA-2G-AAGE    TCGA-2G-AAGF 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGG    TCGA-2G-AAGI    TCGA-2G-AAGJ    TCGA-2G-AAGK    TCGA-2G-AAGM 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGN    TCGA-2G-AAGO    TCGA-2G-AAGP    TCGA-2G-AAGS    TCGA-2G-AAGW 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGX    TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH2    TCGA-2G-AAHG 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT    TCGA-2G-AAKG 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAL5    TCGA-2G-AAL7    TCGA-4K-AA1G    TCGA-4K-AA1H    TCGA-4K-AA1I 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-4K-AAAL    TCGA-SO-A8JP    TCGA-VF-A8A8    TCGA-VF-A8AA    TCGA-VF-A8AB 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-X3-A8G4 
"HTT WILD-TYPE" 
D34V6, binary
               cls
clus              0   1
  HTT MUTATED     3   0
  HTT WILD-TYPE 110   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  HTT MUTATED      3    0
  HTT WILD-TYPE  110    4
   clus
vv  HTT MUTATED HTT WILD-TYPE
  0           3           110
  1           0             4
[1] 2 2
[1] FALSE
D34V7, binary
               cls
clus              0   1
  HTT MUTATED     2   1
  HTT WILD-TYPE 106  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  HTT MUTATED      2    1
  HTT WILD-TYPE  106   20
     clus
vv    HTT MUTATED HTT WILD-TYPE
  NO            2           106
  YES           1            20
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "HTT MUTATED"           
clus
  HTT MUTATED HTT WILD-TYPE 
            2            99 
   TCGA-2G-AAG0    TCGA-2G-AAG3    TCGA-ZM-AA0E    TCGA-2G-AAEX    TCGA-2G-AAF1 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAF4    TCGA-2G-AAF6    TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAFJ    TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAFV    TCGA-2G-AAFY    TCGA-2G-AAFZ    TCGA-2G-AAG5    TCGA-2G-AAG6 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAG7    TCGA-2G-AAG8    TCGA-2G-AAG9    TCGA-2G-AAGA    TCGA-2G-AAGC 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGE    TCGA-2G-AAGF    TCGA-2G-AAGG    TCGA-2G-AAGI    TCGA-2G-AAGJ 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGK    TCGA-2G-AAGM    TCGA-2G-AAGN    TCGA-2G-AAGO    TCGA-2G-AAGP 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGS    TCGA-2G-AAGT    TCGA-2G-AAGV    TCGA-2G-AAGW    TCGA-2G-AAGX 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH0    TCGA-2G-AAH2    TCGA-2G-AAH3 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAH4    TCGA-2G-AAH8    TCGA-2G-AAHA    TCGA-2G-AAHC    TCGA-2G-AAHG 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT    TCGA-2G-AAKD 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAKG    TCGA-2G-AAKH    TCGA-2G-AAKL    TCGA-2G-AAKM    TCGA-2G-AAL5 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAL7    TCGA-2G-AALP    TCGA-2X-A9D5    TCGA-2X-A9D6    TCGA-4K-AA1G 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-4K-AA1H    TCGA-4K-AAAL    TCGA-S6-A8JW    TCGA-S6-A8JX    TCGA-SB-A6J6 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-SB-A76C    TCGA-SN-A84Y    TCGA-SO-A8JP    TCGA-WZ-A7V3    TCGA-WZ-A7V4 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-WZ-A7V5    TCGA-WZ-A8D5    TCGA-XE-A8H1    TCGA-XE-A8H4    TCGA-XE-A8H5 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-XE-A9SE    TCGA-XE-AANI    TCGA-XE-AANJ    TCGA-XE-AANR    TCGA-XE-AANV 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-XE-AAO3    TCGA-XE-AAO4    TCGA-XE-AAO6    TCGA-XE-AAOC    TCGA-XE-AAOD 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-XE-AAOF    TCGA-XE-AAOJ    TCGA-XE-AAOL    TCGA-ZM-AA05    TCGA-ZM-AA06 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-ZM-AA0B    TCGA-ZM-AA0D    TCGA-ZM-AA0F    TCGA-ZM-AA0N 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTT MUTATED       0                         0     3
  HTT WILD-TYPE     4                         6   113
D34V9, multiclass
                           clus
vv                          HTT MUTATED HTT WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D34V10, binary
               cls
clus              0   1
  HTT MUTATED     1   2
  HTT WILD-TYPE  11 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  HTT MUTATED      1    2
  HTT WILD-TYPE   11  107
                        clus
vv                       HTT MUTATED HTT WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO           2           107
[1] 2 2
[1] FALSE

Clustering(35) Variable = EZH2 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED     4   0
  EZH2 WILD-TYPE 123   4
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            127 
  EZH2 MUTATED EZH2 WILD-TYPE 
             0              4 
$`EZH2 MUTATED`
TCGA-2G-AAFN TCGA-VF-A8AD TCGA-WZ-A7V5 TCGA-XE-A8H4 
       25.41        33.07        34.88        18.38 

$`EZH2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       26.04        24.66        16.54        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE 
       17.75        37.18        37.68        24.99        35.61        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52        24.26        24.76        29.39        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  EZH2 MUTATED EZH2 WILD-TYPE 
         18.38           0.10 
  EZH2 MUTATED EZH2 WILD-TYPE 
         34.88         244.50 
  EZH2 MUTATED EZH2 WILD-TYPE 
         29.24          44.48 
[1] "18.4 - 34.9 (29.2)" "0.1 - 244.5 (44.5)"
[1] "hr="     "2.5e+07"
D35V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EZH2 MUTATED    0       1        1        1        0         0         0
  EZH2 WILD-TYPE 46      17       24       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EZH2 MUTATED           0         0          0          1          0
  EZH2 WILD-TYPE         1         2          1          5          5
D35V3, multiclass
            clus
vv           EZH2 MUTATED EZH2 WILD-TYPE
  IS                    0             46
  STAGE I               1             17
  STAGE IA              1             24
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            0              5
[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             T1 T2 T3
  EZH2 MUTATED    0  3  0
  EZH2 WILD-TYPE 74 47  6
D35V4, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  T1            0             74
  T2            3             47
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  EZH2 MUTATED    0     1
  EZH2 WILD-TYPE 45    11
D35V5, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             1             56 
    TCGA-2G-AAG0     TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAF4     TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAFH     TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAFM     TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAG5     TCGA-2G-AAG6     TCGA-2G-AAG7     TCGA-2G-AAG8 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAG9     TCGA-2G-AAGA     TCGA-2G-AAGC     TCGA-2G-AAGE 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAGF     TCGA-2G-AAGG     TCGA-2G-AAGI     TCGA-2G-AAGJ 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAGK     TCGA-2G-AAGM     TCGA-2G-AAGN     TCGA-2G-AAGO 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAGP     TCGA-2G-AAGS     TCGA-2G-AAGW     TCGA-2G-AAGX 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAGY     TCGA-2G-AAGZ     TCGA-2G-AAH2     TCGA-2G-AAHG 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAHL     TCGA-2G-AAHN     TCGA-2G-AAHP     TCGA-2G-AAHT 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAKG     TCGA-2G-AAL5     TCGA-2G-AAL7     TCGA-4K-AA1G 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-4K-AA1H     TCGA-4K-AA1I     TCGA-4K-AAAL     TCGA-SO-A8JP 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-VF-A8A8     TCGA-VF-A8AA     TCGA-VF-A8AB     TCGA-X3-A8G4 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
D35V6, binary
                cls
clus               0   1
  EZH2 MUTATED     3   0
  EZH2 WILD-TYPE 110   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      3    0
  EZH2 WILD-TYPE  110    4
   clus
vv  EZH2 MUTATED EZH2 WILD-TYPE
  0            3            110
  1            0              4
[1] 2 2
[1] FALSE
D35V7, binary
                cls
clus               0   1
  EZH2 MUTATED     2   2
  EZH2 WILD-TYPE 106  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      2    2
  EZH2 WILD-TYPE  106   19
     clus
vv    EZH2 MUTATED EZH2 WILD-TYPE
  NO             2            106
  YES            2             19
[1] 2 2
[1] FALSE
D35V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED       0                         0     4
  EZH2 WILD-TYPE     4                         6   112
D35V9, multiclass
                           clus
vv                          EZH2 MUTATED EZH2 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D35V10, binary
                cls
clus               0   1
  EZH2 MUTATED     0   4
  EZH2 WILD-TYPE  12 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      0    4
  EZH2 WILD-TYPE   12  105
                        clus
vv                       EZH2 MUTATED EZH2 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            4            105
[1] 2 2
[1] FALSE

Clustering(36) Variable = PABPC3 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  PABPC3 MUTATED     3   0
  PABPC3 WILD-TYPE 124   4
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              128 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               0                4 
$`PABPC3 MUTATED`
TCGA-2G-AAGX TCGA-4K-AA1I TCGA-4K-AAAL 
      181.28         0.10        15.88 

$`PABPC3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      132.10       158.33       144.85       148.83       161.06       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       17.03        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  PABPC3 MUTATED PABPC3 WILD-TYPE 
            0.10             0.43 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
          181.28           244.50 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
          15.880           41.605 
[1] "0.1 - 181.3 (15.9)" "0.4 - 244.5 (41.6)"
[1] "hr="     "9100000"
D36V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PABPC3 MUTATED    1       0        2        0        0         0         0
  PABPC3 WILD-TYPE 45      18       23       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PABPC3 MUTATED           0         0          0          0          0
  PABPC3 WILD-TYPE         1         2          1          6          5
D36V3, multiclass
            clus
vv           PABPC3 MUTATED PABPC3 WILD-TYPE
  IS                      1               45
  STAGE I                 0               18
  STAGE IA                2               23
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  PABPC3 MUTATED    2  1  0
  PABPC3 WILD-TYPE 72 49  6
D36V4, multiclass
    clus
vv   PABPC3 MUTATED PABPC3 WILD-TYPE
  T1              2               72
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PABPC3 MUTATED    3     0
  PABPC3 WILD-TYPE 42    12
D36V5, multiclass
       clus
vv      PABPC3 MUTATED PABPC3 WILD-TYPE
  N0                 3               42
  N1+N2              0               12
[1] 2 2
[1] FALSE
D36V6, binary
                  cls
clus                 0   1
  PABPC3 MUTATED     3   0
  PABPC3 WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      3    0
  PABPC3 WILD-TYPE  110    4
   clus
vv  PABPC3 MUTATED PABPC3 WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                 0   1
  PABPC3 MUTATED     3   0
  PABPC3 WILD-TYPE 105  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      3    0
  PABPC3 WILD-TYPE  105   21
     clus
vv    PABPC3 MUTATED PABPC3 WILD-TYPE
  NO               3              105
  YES              0               21
[1] 2 2
[1] FALSE
D36V8, continuous
[1] "Remove cluster labels:" "PABPC3 MUTATED"        
clus
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               2               99 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEX 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0       TCGA-2G-AAH2 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8       TCGA-2G-AAHA 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-S6-A8JW       TCGA-S6-A8JX 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-SB-A6J6       TCGA-SB-A76C       TCGA-SN-A84Y       TCGA-SO-A8JP 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5       TCGA-WZ-A8D5 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5       TCGA-XE-A9SE 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR       TCGA-XE-AANV 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6       TCGA-XE-AAOC 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ       TCGA-XE-AAOL 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B       TCGA-ZM-AA0D 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
      TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" "PABPC3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC3 MUTATED       0                         0     3
  PABPC3 WILD-TYPE     4                         6   113
D36V9, multiclass
                           clus
vv                          PABPC3 MUTATED PABPC3 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D36V10, binary
                  cls
clus                 0   1
  PABPC3 MUTATED     0   3
  PABPC3 WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      0    3
  PABPC3 WILD-TYPE   12  106
                        clus
vv                       PABPC3 MUTATED PABPC3 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(37) Variable = CUX1 MUTATION ANALYSIS
D37V1, survival
                sevent
clus2              0   1
  CUX1 MUTATED     5   0
  CUX1 WILD-TYPE 122   4
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            126 
  CUX1 MUTATED CUX1 WILD-TYPE 
             0              4 
$`CUX1 MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-VF-A8A8 TCGA-VF-A8AC 
       76.11        26.04        45.67        37.18        35.61 

$`CUX1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
      114.77       128.58       203.28        45.21        22.19        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 
       16.54        25.41        22.52        36.13        44.48        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       81.47        89.88        85.84       103.13        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      199.23        59.90       204.16        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA 
       16.31         9.63        10.26        17.23        17.75        37.68 
TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       24.99        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  CUX1 MUTATED CUX1 WILD-TYPE 
         26.04           0.10 
  CUX1 MUTATED CUX1 WILD-TYPE 
         76.11         244.50 
  CUX1 MUTATED CUX1 WILD-TYPE 
        37.180         41.605 
[1] "26.0 - 76.1 (37.2)" "0.1 - 244.5 (41.6)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUX1 MUTATED    1       1        2        0        0         0         0
  CUX1 WILD-TYPE 45      17       23       11        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CUX1 MUTATED           0         0          0          0          0
  CUX1 WILD-TYPE         1         2          1          6          5
D37V3, multiclass
            clus
vv           CUX1 MUTATED CUX1 WILD-TYPE
  IS                    1             45
  STAGE I               1             17
  STAGE IA              2             23
  STAGE IB              0             11
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  CUX1 MUTATED    5  0  0
  CUX1 WILD-TYPE 69 50  6
D37V4, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  T1            5             69
  T2            0             50
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  CUX1 MUTATED    4     0
  CUX1 WILD-TYPE 41    12
D37V5, multiclass
       clus
vv      CUX1 MUTATED CUX1 WILD-TYPE
  N0               4             41
  N1+N2            0             12
[1] 2 2
[1] FALSE
D37V6, binary
                cls
clus               0   1
  CUX1 MUTATED     5   0
  CUX1 WILD-TYPE 108   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      5    0
  CUX1 WILD-TYPE  108    4
   clus
vv  CUX1 MUTATED CUX1 WILD-TYPE
  0            5            108
  1            0              4
[1] 2 2
[1] FALSE
D37V7, binary
                cls
clus               0   1
  CUX1 MUTATED     4   1
  CUX1 WILD-TYPE 104  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      4    1
  CUX1 WILD-TYPE  104   20
     clus
vv    CUX1 MUTATED CUX1 WILD-TYPE
  NO             4            104
  YES            1             20
[1] 2 2
[1] FALSE
D37V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUX1 MUTATED       1                         0     4
  CUX1 WILD-TYPE     3                         6   112
D37V9, multiclass
                           clus
vv                          CUX1 MUTATED CUX1 WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D37V10, binary
                cls
clus               0   1
  CUX1 MUTATED     0   5
  CUX1 WILD-TYPE  12 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      0    5
  CUX1 WILD-TYPE   12  104
                        clus
vv                       CUX1 MUTATED CUX1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(38) Variable = DLC1 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 124   4
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            128 
  DLC1 MUTATED DLC1 WILD-TYPE 
             0              4 
$`DLC1 MUTATED`
TCGA-2G-AAGJ TCGA-2X-A9D6 TCGA-SO-A8JP 
       96.59        19.96        17.75 

$`DLC1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
      103.13       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H 
      244.50       131.21        86.96        14.30        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 
        1.38        16.31         9.63        10.26        17.23        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  DLC1 MUTATED DLC1 WILD-TYPE 
         17.75           0.10 
  DLC1 MUTATED DLC1 WILD-TYPE 
         96.59         244.50 
  DLC1 MUTATED DLC1 WILD-TYPE 
        19.960         41.605 
[1] "17.8 - 96.6 (20.0)" "0.1 - 244.5 (41.6)"
[1] "hr="     "9200000"
D38V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLC1 MUTATED    0       2        1        0        0         0         0
  DLC1 WILD-TYPE 46      16       24       11        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DLC1 MUTATED           0         0          0          0          0
  DLC1 WILD-TYPE         1         2          1          6          5
D38V3, multiclass
            clus
vv           DLC1 MUTATED DLC1 WILD-TYPE
  IS                    0             46
  STAGE I               2             16
  STAGE IA              1             24
  STAGE IB              0             11
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  DLC1 MUTATED    3  0  0
  DLC1 WILD-TYPE 71 50  6
D38V4, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  T1            3             71
  T2            0             50
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  DLC1 MUTATED    2     0
  DLC1 WILD-TYPE 43    12
D38V5, multiclass
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2             55 
    TCGA-2G-AAG0     TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAF4     TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAFH     TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAFM     TCGA-2G-AAFN     TCGA-2G-AAFO     TCGA-2G-AAFV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAFY     TCGA-2G-AAG5     TCGA-2G-AAG6     TCGA-2G-AAG7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAG8     TCGA-2G-AAG9     TCGA-2G-AAGA     TCGA-2G-AAGC 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAGE     TCGA-2G-AAGF     TCGA-2G-AAGG     TCGA-2G-AAGI 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAGK     TCGA-2G-AAGM     TCGA-2G-AAGN     TCGA-2G-AAGO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAGP     TCGA-2G-AAGS     TCGA-2G-AAGW     TCGA-2G-AAGX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAGY     TCGA-2G-AAGZ     TCGA-2G-AAH2     TCGA-2G-AAHG 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAHL     TCGA-2G-AAHN     TCGA-2G-AAHP     TCGA-2G-AAHT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAKG     TCGA-2G-AAL5     TCGA-2G-AAL7     TCGA-4K-AA1G 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-4K-AA1H     TCGA-4K-AA1I     TCGA-4K-AAAL     TCGA-VF-A8A8 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-VF-A8AA     TCGA-VF-A8AB     TCGA-X3-A8G4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
D38V6, binary
                cls
clus               0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 110   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    0
  DLC1 WILD-TYPE  110    4
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            3            110
  1            0              4
[1] 2 2
[1] FALSE
D38V7, binary
                cls
clus               0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 105  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    0
  DLC1 WILD-TYPE  105   21
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             3            105
  YES            0             21
[1] 2 2
[1] FALSE
D38V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED       0                         1     2
  DLC1 WILD-TYPE     4                         5   114
D38V9, multiclass
                           clus
vv                          DLC1 MUTATED DLC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                                2            114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                cls
clus               0   1
  DLC1 MUTATED     0   3
  DLC1 WILD-TYPE  12 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      0    3
  DLC1 WILD-TYPE   12  106
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3            106
[1] 2 2
[1] FALSE

Clustering(39) Variable = STAB1 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  STAB1 MUTATED     7   0
  STAB1 WILD-TYPE 120   4
  STAB1 MUTATED STAB1 WILD-TYPE 
              7             124 
  STAB1 MUTATED STAB1 WILD-TYPE 
              0               4 
$`STAB1 MUTATED`
TCGA-2G-AAFH TCGA-2G-AAGO TCGA-4K-AA1H TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-XE-AAOF 
       45.21       132.36        17.03        17.23        37.18        41.69 
TCGA-ZM-AA0F 
       22.39 

$`STAB1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ 
       76.11       114.77       128.58       203.28        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGP TCGA-2G-AAGS 
       96.59       119.05       127.92       120.20       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I 
      131.21        86.96        14.30        19.96        14.33         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB 
       16.31         9.63        10.26        17.75        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43        15.48        22.09        27.72         9.24 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       68.02        64.57        31.92        36.59         0.56        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       71.24        17.62        51.72        28.41        37.02        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        27.88        57.07        20.84 

  STAB1 MUTATED STAB1 WILD-TYPE 
          17.03            0.10 
  STAB1 MUTATED STAB1 WILD-TYPE 
         132.36          244.50 
  STAB1 MUTATED STAB1 WILD-TYPE 
          37.18           43.00 
[1] "17.0 - 132.4 (37.2)" "0.1 - 244.5 (43.0)" 
[1] "hr="     "2.6e+07"
D39V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAB1 MUTATED    2       0        4        0        0         0         1
  STAB1 WILD-TYPE 44      18       21       11        4         5         0
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  STAB1 MUTATED           0         0          0          0          0
  STAB1 WILD-TYPE         1         2          1          6          5
D39V3, multiclass
            clus
vv           STAB1 MUTATED STAB1 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               4              21
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              1               0
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  STAB1 MUTATED    4  3  0
  STAB1 WILD-TYPE 70 47  6
D39V4, multiclass
    clus
vv   STAB1 MUTATED STAB1 WILD-TYPE
  T1             4              70
  T2             3              47
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  STAB1 MUTATED    3     1
  STAB1 WILD-TYPE 42    11
D39V5, multiclass
       clus
vv      STAB1 MUTATED STAB1 WILD-TYPE
  N0                3              42
  N1+N2             1              11
[1] 2 2
[1] FALSE
D39V6, binary
                 cls
clus                0   1
  STAB1 MUTATED     7   0
  STAB1 WILD-TYPE 106   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED      7    0
  STAB1 WILD-TYPE  106    4
   clus
vv  STAB1 MUTATED STAB1 WILD-TYPE
  0             7             106
  1             0               4
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus                0   1
  STAB1 MUTATED     6   1
  STAB1 WILD-TYPE 102  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED      6    1
  STAB1 WILD-TYPE  102   20
     clus
vv    STAB1 MUTATED STAB1 WILD-TYPE
  NO              6             102
  YES             1              20
[1] 2 2
[1] FALSE
D39V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAB1 MUTATED       1                         0     6
  STAB1 WILD-TYPE     3                         6   110
D39V9, multiclass
                           clus
vv                          STAB1 MUTATED STAB1 WILD-TYPE
  ASIAN                                 1               3
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 6             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"
D39V10, binary
                 cls
clus                0   1
  STAB1 MUTATED     1   6
  STAB1 WILD-TYPE  11 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB1 MUTATED      1    6
  STAB1 WILD-TYPE   11  103
                        clus
vv                       STAB1 MUTATED STAB1 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             6             103
[1] 2 2
[1] FALSE

Clustering(40) Variable = NOTCH1 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED     5   0
  NOTCH1 WILD-TYPE 122   4
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               5              126 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               0                4 
$`NOTCH1 MUTATED`
TCGA-2G-AAFG TCGA-VF-A8A8 TCGA-VF-A8AE TCGA-XE-A8H5 TCGA-XE-AAOD 
      203.28        37.18        23.90        40.01        67.66 

$`NOTCH1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
       76.11       114.77       128.58        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 
       17.75        37.68        24.99        35.61        33.07        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            23.9              0.1 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          203.28           244.50 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          40.010           41.605 
[1] "23.9 - 203.3 (40.0)" "0.1 - 244.5 (41.6)" 
[1] "hr="     "2.6e+07"
D40V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOTCH1 MUTATED    2       0        2        1        0         0         0
  NOTCH1 WILD-TYPE 44      18       23       10        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NOTCH1 MUTATED           0         0          0          0          0
  NOTCH1 WILD-TYPE         1         2          1          6          5
D40V3, multiclass
            clus
vv           NOTCH1 MUTATED NOTCH1 WILD-TYPE
  IS                      2               44
  STAGE I                 0               18
  STAGE IA                2               23
  STAGE IB                1               10
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  NOTCH1 MUTATED    4  1  0
  NOTCH1 WILD-TYPE 70 49  6
D40V4, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T1              4               70
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  NOTCH1 MUTATED    2     0
  NOTCH1 WILD-TYPE 43    12
D40V5, multiclass
[1] "Remove cluster labels:" "NOTCH1 MUTATED"        
clus
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
               2               55 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFH 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
      TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" "NOTCH1 WILD-TYPE" 
D40V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     5   0
  NOTCH1 WILD-TYPE 108   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      5    0
  NOTCH1 WILD-TYPE  108    4
   clus
vv  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  0              5              108
  1              0                4
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     3   2
  NOTCH1 WILD-TYPE 105  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      3    2
  NOTCH1 WILD-TYPE  105   19
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO               3              105
  YES              2               19
[1] 2 2
[1] FALSE
D40V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH1 MUTATED       0                         0     4
  NOTCH1 WILD-TYPE     4                         6   112
D40V9, multiclass
                           clus
vv                          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D40V10, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     1   4
  NOTCH1 WILD-TYPE  11 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      1    4
  NOTCH1 WILD-TYPE   11  105
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              4              105
[1] 2 2
[1] FALSE

Clustering(41) Variable = AHDC1 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  AHDC1 MUTATED     3   0
  AHDC1 WILD-TYPE 124   4
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             128 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              0               4 
$`AHDC1 MUTATED`
TCGA-2G-AAG5 TCGA-2G-AAGM TCGA-2G-AAH4 
       75.58       127.92       204.16 

$`AHDC1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       36.13        44.48        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       96.59       119.05       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      180.07       199.23        59.90        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80       232.80       211.89       186.31        17.82       208.44 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      216.92       225.60       230.89       229.22       244.50       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       86.96        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
       15.88        22.95        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  AHDC1 MUTATED AHDC1 WILD-TYPE 
          75.58            0.10 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
         204.16          244.50 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
         127.92           40.70 
[1] "75.6 - 204.2 (127.9)" "0.1 - 244.5 (40.7)"  
[1] "hr="     "9300000"
D41V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AHDC1 MUTATED    2       0        0        0        1         0         0
  AHDC1 WILD-TYPE 44      18       25       11        3         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AHDC1 MUTATED           0         0          0          0          0
  AHDC1 WILD-TYPE         1         2          1          6          5
D41V3, multiclass
            clus
vv           AHDC1 MUTATED AHDC1 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               0              25
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  AHDC1 MUTATED    2  1  0
  AHDC1 WILD-TYPE 72 49  6
D41V4, multiclass
    clus
vv   AHDC1 MUTATED AHDC1 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  AHDC1 MUTATED    2     0
  AHDC1 WILD-TYPE 43    12
D41V5, multiclass
[1] "Remove cluster labels:" "AHDC1 MUTATED"         
clus
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAGK      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGW      TCGA-2G-AAGX      TCGA-2G-AAGY 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG      TCGA-2G-AAHL 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKG 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G      TCGA-4K-AA1H 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP      TCGA-VF-A8A8 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
D41V6, binary
                 cls
clus                0   1
  AHDC1 MUTATED     3   0
  AHDC1 WILD-TYPE 110   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      3    0
  AHDC1 WILD-TYPE  110    4
   clus
vv  AHDC1 MUTATED AHDC1 WILD-TYPE
  0             3             110
  1             0               4
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  AHDC1 MUTATED     3   0
  AHDC1 WILD-TYPE 105  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      3    0
  AHDC1 WILD-TYPE  105   21
     clus
vv    AHDC1 MUTATED AHDC1 WILD-TYPE
  NO              3             105
  YES             0              21
[1] 2 2
[1] FALSE
D41V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AHDC1 MUTATED       0                         0     3
  AHDC1 WILD-TYPE     4                         6   113
D41V9, multiclass
                           clus
vv                          AHDC1 MUTATED AHDC1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D41V10, binary
                 cls
clus                0   1
  AHDC1 MUTATED     0   3
  AHDC1 WILD-TYPE  12 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      0    3
  AHDC1 WILD-TYPE   12  106
                        clus
vv                       AHDC1 MUTATED AHDC1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(42) Variable = EPAS1 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  EPAS1 MUTATED     4   0
  EPAS1 WILD-TYPE 123   4
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             127 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              0               4 
$`EPAS1 MUTATED`
TCGA-2G-AAH4 TCGA-4K-AA1I TCGA-VF-A8A8 TCGA-XE-A8H4 
      204.16         0.10        37.18        18.38 

$`EPAS1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 
      175.20       172.04       180.07       199.23        59.90        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
       17.03        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  EPAS1 MUTATED EPAS1 WILD-TYPE 
           0.10            0.43 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         204.16          244.50 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
          27.78           41.69 
[1] "0.1 - 204.2 (27.8)" "0.4 - 244.5 (41.7)"
[1] "hr="     "9200000"
D42V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPAS1 MUTATED    0       0        3        0        1         0         0
  EPAS1 WILD-TYPE 46      18       22       11        3         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EPAS1 MUTATED           0         0          0          0          0
  EPAS1 WILD-TYPE         1         2          1          6          5
D42V3, multiclass
            clus
vv           EPAS1 MUTATED EPAS1 WILD-TYPE
  IS                     0              46
  STAGE I                0              18
  STAGE IA               3              22
  STAGE IB               0              11
  STAGE II               1               3
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  EPAS1 MUTATED    3  0  0
  EPAS1 WILD-TYPE 71 50  6
D42V4, multiclass
    clus
vv   EPAS1 MUTATED EPAS1 WILD-TYPE
  T1             3              71
  T2             0              50
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  EPAS1 MUTATED    2     0
  EPAS1 WILD-TYPE 43    12
D42V5, multiclass
[1] "Remove cluster labels:" "EPAS1 MUTATED"         
clus
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGW 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAHT      TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AAAL      TCGA-SO-A8JP 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
D42V6, binary
                 cls
clus                0   1
  EPAS1 MUTATED     4   0
  EPAS1 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      4    0
  EPAS1 WILD-TYPE  109    4
   clus
vv  EPAS1 MUTATED EPAS1 WILD-TYPE
  0             4             109
  1             0               4
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  EPAS1 MUTATED     3   1
  EPAS1 WILD-TYPE 105  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      3    1
  EPAS1 WILD-TYPE  105   20
     clus
vv    EPAS1 MUTATED EPAS1 WILD-TYPE
  NO              3             105
  YES             1              20
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "EPAS1 MUTATED"         
clus
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              2              99 
     TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-ZM-AA0E      TCGA-2G-AAEX 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAF1      TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFG      TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFL      TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFV      TCGA-2G-AAFY      TCGA-2G-AAFZ      TCGA-2G-AAG5 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8      TCGA-2G-AAG9 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE      TCGA-2G-AAGF 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGT      TCGA-2G-AAGV      TCGA-2G-AAGW 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH0 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAH2      TCGA-2G-AAH3      TCGA-2G-AAH8      TCGA-2G-AAHA 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAHC      TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHN 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKD      TCGA-2G-AAKG 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAKH      TCGA-2G-AAKL      TCGA-2G-AAKM      TCGA-2G-AAL5 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAL7      TCGA-2G-AALP      TCGA-2X-A9D5      TCGA-2X-A9D6 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AAAL      TCGA-S6-A8JW 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-S6-A8JX      TCGA-SB-A6J6      TCGA-SB-A76C      TCGA-SN-A84Y 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-SO-A8JP      TCGA-WZ-A7V3      TCGA-WZ-A7V4      TCGA-WZ-A7V5 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-WZ-A8D5      TCGA-XE-A8H1      TCGA-XE-A8H5      TCGA-XE-A9SE 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-XE-AANI      TCGA-XE-AANJ      TCGA-XE-AANR      TCGA-XE-AANV 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-XE-AAO3      TCGA-XE-AAO4      TCGA-XE-AAO6      TCGA-XE-AAOC 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-XE-AAOD      TCGA-XE-AAOF      TCGA-XE-AAOJ      TCGA-XE-AAOL 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-ZM-AA05      TCGA-ZM-AA06      TCGA-ZM-AA0B      TCGA-ZM-AA0D 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPAS1 MUTATED       0                         0     4
  EPAS1 WILD-TYPE     4                         6   112
D42V9, multiclass
                           clus
vv                          EPAS1 MUTATED EPAS1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D42V10, binary
                 cls
clus                0   1
  EPAS1 MUTATED     0   4
  EPAS1 WILD-TYPE  12 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      0    4
  EPAS1 WILD-TYPE   12  105
                        clus
vv                       EPAS1 MUTATED EPAS1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(43) Variable = PIK3CD MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  PIK3CD MUTATED     2   1
  PIK3CD WILD-TYPE 125   3
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              128 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               1                3 
$`PIK3CD MUTATED`
TCGA-2G-AAEW TCGA-VF-A8AA TCGA-WZ-A7V4 
       20.32        37.68        29.39 

$`PIK3CD WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       17.75        37.18        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52        24.26        24.76        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  PIK3CD MUTATED PIK3CD WILD-TYPE 
           20.32             0.10 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
           37.68           244.50 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
          29.390           43.085 
[1] "20.3 - 37.7 (29.4)" "0.1 - 244.5 (43.1)"
[1] "hr=" "18" 
D43V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CD MUTATED    1       2        0        0        0         0         0
  PIK3CD WILD-TYPE 45      16       25       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PIK3CD MUTATED           0         0          0          0          0
  PIK3CD WILD-TYPE         1         2          1          6          5
D43V3, multiclass
            clus
vv           PIK3CD MUTATED PIK3CD WILD-TYPE
  IS                      1               45
  STAGE I                 2               16
  STAGE IA                0               25
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  PIK3CD MUTATED    3  0  0
  PIK3CD WILD-TYPE 71 50  6
D43V4, multiclass
    clus
vv   PIK3CD MUTATED PIK3CD WILD-TYPE
  T1              3               71
  T2              0               50
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PIK3CD MUTATED    2     0
  PIK3CD WILD-TYPE 43    12
D43V5, multiclass
[1] "Remove cluster labels:" "PIK3CD MUTATED"        
clus
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               2               55 
      TCGA-2G-AAG0       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AB       TCGA-X3-A8G4 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
D43V6, binary
                  cls
clus                 0   1
  PIK3CD MUTATED     2   0
  PIK3CD WILD-TYPE 111   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CD MUTATED      2    0
  PIK3CD WILD-TYPE  111    4
   clus
vv  PIK3CD MUTATED PIK3CD WILD-TYPE
  0              2              111
  1              0                4
[1] 2 2
[1] FALSE
D43V7, binary
                  cls
clus                 0   1
  PIK3CD MUTATED     3   0
  PIK3CD WILD-TYPE 105  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CD MUTATED      3    0
  PIK3CD WILD-TYPE  105   21
     clus
vv    PIK3CD MUTATED PIK3CD WILD-TYPE
  NO               3              105
  YES              0               21
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "PIK3CD MUTATED"        
clus
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               1              100 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEX 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAH2       TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAHA       TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2X-A9D6       TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AAAL 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-S6-A8JW       TCGA-S6-A8JX       TCGA-SB-A6J6       TCGA-SB-A76C 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-SN-A84Y       TCGA-SO-A8JP       TCGA-WZ-A7V3       TCGA-WZ-A7V5 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-WZ-A8D5       TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-XE-A9SE       TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-XE-AANV       TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-XE-AAOC       TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-XE-AAOL       TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-ZM-AA0D       TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CD MUTATED       0                         0     3
  PIK3CD WILD-TYPE     4                         6   113
D43V9, multiclass
                           clus
vv                          PIK3CD MUTATED PIK3CD WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D43V10, binary
                  cls
clus                 0   1
  PIK3CD MUTATED     0   3
  PIK3CD WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CD MUTATED      0    3
  PIK3CD WILD-TYPE   12  106
                        clus
vv                       PIK3CD MUTATED PIK3CD WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(44) Variable = BCL11B MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  BCL11B MUTATED     5   0
  BCL11B WILD-TYPE 122   4
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              126 
  BCL11B MUTATED BCL11B WILD-TYPE 
               0                4 
$`BCL11B MUTATED`
TCGA-2G-AAG3 TCGA-XE-AAOF TCGA-YU-A90S TCGA-YU-A90W TCGA-ZM-AA06 
       52.37        41.69        31.92        36.59        49.25 

$`BCL11B WILD-TYPE`
TCGA-2G-AAG0 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.75        37.18        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 
       23.90        41.52        24.26        24.76        29.39        34.88 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE 
       25.45        28.14         6.87        18.38        40.01        23.28 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        55.92        93.93        12.07 
TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL 
        7.89        16.87         8.88        67.66        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       37.02        27.55        27.88        22.39        57.07        20.84 

  BCL11B MUTATED BCL11B WILD-TYPE 
           31.92             0.10 
  BCL11B MUTATED BCL11B WILD-TYPE 
           52.37           244.50 
  BCL11B MUTATED BCL11B WILD-TYPE 
          41.690           41.455 
[1] "31.9 - 52.4 (41.7)" "0.1 - 244.5 (41.5)"
[1] "hr="     "2.6e+07"
D44V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL11B MUTATED    1       0        3        1        0         0         0
  BCL11B WILD-TYPE 45      18       22       10        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BCL11B MUTATED           0         0          0          0          0
  BCL11B WILD-TYPE         1         2          1          6          5
D44V3, multiclass
            clus
vv           BCL11B MUTATED BCL11B WILD-TYPE
  IS                      1               45
  STAGE I                 0               18
  STAGE IA                3               22
  STAGE IB                1               10
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  BCL11B MUTATED    3  2  0
  BCL11B WILD-TYPE 71 48  6
D44V4, multiclass
    clus
vv   BCL11B MUTATED BCL11B WILD-TYPE
  T1              3               71
  T2              2               48
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  BCL11B MUTATED    0     0
  BCL11B WILD-TYPE 45    12
D44V5, multiclass
D44V6, binary
                  cls
clus                 0   1
  BCL11B MUTATED     3   0
  BCL11B WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11B MUTATED      3    0
  BCL11B WILD-TYPE  110    4
   clus
vv  BCL11B MUTATED BCL11B WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D44V7, binary
                  cls
clus                 0   1
  BCL11B MUTATED     2   3
  BCL11B WILD-TYPE 106  18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11B MUTATED      2    3
  BCL11B WILD-TYPE  106   18
     clus
vv    BCL11B MUTATED BCL11B WILD-TYPE
  NO               2              106
  YES              3               18
[1] 2 2
[1] FALSE
D44V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL11B MUTATED       1                         0     4
  BCL11B WILD-TYPE     3                         6   112
D44V9, multiclass
                           clus
vv                          BCL11B MUTATED BCL11B WILD-TYPE
  ASIAN                                  1                3
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D44V10, binary
                  cls
clus                 0   1
  BCL11B MUTATED     0   3
  BCL11B WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11B MUTATED      0    3
  BCL11B WILD-TYPE   12  106
                        clus
vv                       BCL11B MUTATED BCL11B WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(45) Variable = KIAA0430 MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                  0   1
  KIAA0430 MUTATED     3   0
  KIAA0430 WILD-TYPE 124   4
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 3                128 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 0                  4 
$`KIAA0430 MUTATED`
TCGA-2G-AAFY TCGA-2X-A9D5 TCGA-XE-A8H4 
       36.13        14.30        18.38 

$`KIAA0430 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      244.50       131.21        86.96        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
              14.3                0.1 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
             36.13             244.50 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
            18.380             43.085 
[1] "14.3 - 36.1 (18.4)" "0.1 - 244.5 (43.1)"
[1] "hr="     "9200000"
D45V2, continuous
                    vv
clus                 IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0430 MUTATED    0       1        1        0        0         1         0
  KIAA0430 WILD-TYPE 46      17       24       11        4         4         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KIAA0430 MUTATED           0         0          0          0          0
  KIAA0430 WILD-TYPE         1         2          1          6          5
D45V3, multiclass
            clus
vv           KIAA0430 MUTATED KIAA0430 WILD-TYPE
  IS                        0                 46
  STAGE I                   1                 17
  STAGE IA                  1                 24
  STAGE IB                  0                 11
  STAGE II                  0                  4
  STAGE IIA                 1                  4
  STAGE IIB                 0                  1
  STAGE IIC                 0                  1
  STAGE III                 0                  2
  STAGE IIIA                0                  1
  STAGE IIIB                0                  6
  STAGE IIIC                0                  5
[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                 T1 T2 T3
  KIAA0430 MUTATED    1  1  0
  KIAA0430 WILD-TYPE 73 49  6
D45V4, multiclass
[1] "Remove cluster labels:" "KIAA0430 MUTATED"      
clus
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 2                128 
        TCGA-2G-AAG0         TCGA-2G-AAG3         TCGA-ZM-AA0E 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAEW         TCGA-2G-AAEX         TCGA-2G-AAF1 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAF4         TCGA-2G-AAF6         TCGA-2G-AAF8 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFG         TCGA-2G-AAFH         TCGA-2G-AAFI 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFJ         TCGA-2G-AAFL         TCGA-2G-AAFM 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFN         TCGA-2G-AAFO         TCGA-2G-AAFV 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFZ         TCGA-2G-AAG5         TCGA-2G-AAG6 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAG7         TCGA-2G-AAG8         TCGA-2G-AAG9 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGA         TCGA-2G-AAGC         TCGA-2G-AAGE 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGF         TCGA-2G-AAGG         TCGA-2G-AAGI 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGJ         TCGA-2G-AAGK         TCGA-2G-AAGM 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGN         TCGA-2G-AAGO         TCGA-2G-AAGP 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGS         TCGA-2G-AAGT         TCGA-2G-AAGV 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGW         TCGA-2G-AAGX         TCGA-2G-AAGY 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGZ         TCGA-2G-AAH0         TCGA-2G-AAH2 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAH3         TCGA-2G-AAH4         TCGA-2G-AAH8 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAHA         TCGA-2G-AAHC         TCGA-2G-AAHG 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAHL         TCGA-2G-AAHN         TCGA-2G-AAHP 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAHT         TCGA-2G-AAKD         TCGA-2G-AAKG 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAKH         TCGA-2G-AAKL         TCGA-2G-AAKM 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAL5         TCGA-2G-AAL7         TCGA-2G-AALP 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2X-A9D6         TCGA-4K-AA1G         TCGA-4K-AA1H 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-4K-AA1I         TCGA-4K-AAAL         TCGA-S6-A8JW 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-S6-A8JX         TCGA-S6-A8JY         TCGA-SB-A6J6 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-SB-A76C         TCGA-SN-A6IS         TCGA-SN-A84W 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-SN-A84X         TCGA-SN-A84Y         TCGA-SO-A8JP 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-VF-A8A8         TCGA-VF-A8AA         TCGA-VF-A8AB 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-VF-A8AC         TCGA-VF-A8AD         TCGA-VF-A8AE 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-W4-A7U2         TCGA-W4-A7U4         TCGA-WZ-A7V3 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-WZ-A7V4         TCGA-WZ-A7V5         TCGA-WZ-A8D5 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-X3-A8G4         TCGA-XE-A8H1         TCGA-XE-A8H5 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XE-A9SE         TCGA-XE-AANI         TCGA-XE-AANJ 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XE-AANR         TCGA-XE-AANV         TCGA-XE-AAO3 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XE-AAO4         TCGA-XE-AAO6         TCGA-XE-AAOB 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XE-AAOC         TCGA-XE-AAOD         TCGA-XE-AAOF 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XE-AAOJ         TCGA-XE-AAOL         TCGA-XY-A89B 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-XY-A8S2         TCGA-XY-A8S3         TCGA-XY-A9T9 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-YU-A90P         TCGA-YU-A90Q         TCGA-YU-A90S 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-YU-A90W         TCGA-YU-A90Y         TCGA-YU-A912 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-YU-A94D         TCGA-YU-A94I         TCGA-YU-AA4L 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-YU-AA61         TCGA-ZM-AA05         TCGA-ZM-AA06 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-ZM-AA0B         TCGA-ZM-AA0D         TCGA-ZM-AA0F 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-ZM-AA0H         TCGA-ZM-AA0N 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
                    vv
clus                 N0 N1+N2
  KIAA0430 MUTATED    0     1
  KIAA0430 WILD-TYPE 45    11
D45V5, multiclass
[1] "Remove cluster labels:" "KIAA0430 MUTATED"      
clus
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 1                 56 
        TCGA-2G-AAG0         TCGA-2G-AAEW         TCGA-2G-AAEX 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAF1         TCGA-2G-AAF4         TCGA-2G-AAF6 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAF8         TCGA-2G-AAFG         TCGA-2G-AAFH 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFI         TCGA-2G-AAFJ         TCGA-2G-AAFL 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFM         TCGA-2G-AAFN         TCGA-2G-AAFO 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAFV         TCGA-2G-AAG5         TCGA-2G-AAG6 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAG7         TCGA-2G-AAG8         TCGA-2G-AAG9 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGA         TCGA-2G-AAGC         TCGA-2G-AAGE 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGF         TCGA-2G-AAGG         TCGA-2G-AAGI 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGJ         TCGA-2G-AAGK         TCGA-2G-AAGM 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGN         TCGA-2G-AAGO         TCGA-2G-AAGP 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGS         TCGA-2G-AAGW         TCGA-2G-AAGX 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAGY         TCGA-2G-AAGZ         TCGA-2G-AAH2 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAHG         TCGA-2G-AAHL         TCGA-2G-AAHN 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAHP         TCGA-2G-AAHT         TCGA-2G-AAKG 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-2G-AAL5         TCGA-2G-AAL7         TCGA-4K-AA1G 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-4K-AA1H         TCGA-4K-AA1I         TCGA-4K-AAAL 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-SO-A8JP         TCGA-VF-A8A8         TCGA-VF-A8AA 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
        TCGA-VF-A8AB         TCGA-X3-A8G4 
"KIAA0430 WILD-TYPE" "KIAA0430 WILD-TYPE" 
D45V6, binary
                    cls
clus                   0   1
  KIAA0430 MUTATED     3   0
  KIAA0430 WILD-TYPE 110   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      3    0
  KIAA0430 WILD-TYPE  110    4
   clus
vv  KIAA0430 MUTATED KIAA0430 WILD-TYPE
  0                3                110
  1                0                  4
[1] 2 2
[1] FALSE
D45V7, binary
                    cls
clus                   0   1
  KIAA0430 MUTATED     2   1
  KIAA0430 WILD-TYPE 106  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      2    1
  KIAA0430 WILD-TYPE  106   20
     clus
vv    KIAA0430 MUTATED KIAA0430 WILD-TYPE
  NO                 2                106
  YES                1                 20
[1] 2 2
[1] FALSE
D45V8, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0430 MUTATED       0                         0     3
  KIAA0430 WILD-TYPE     4                         6   113
D45V9, multiclass
                           clus
vv                          KIAA0430 MUTATED KIAA0430 WILD-TYPE
  ASIAN                                    0                  4
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                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"
D45V10, binary
                    cls
clus                   0   1
  KIAA0430 MUTATED     0   3
  KIAA0430 WILD-TYPE  12 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      0    3
  KIAA0430 WILD-TYPE   12  106
                        clus
vv                       KIAA0430 MUTATED KIAA0430 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                106
[1] 2 2
[1] FALSE

Clustering(46) Variable = MTIF3 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  MTIF3 MUTATED     3   0
  MTIF3 WILD-TYPE 124   4
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             128 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              0               4 
$`MTIF3 MUTATED`
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-ZM-AA0D 
       40.01        34.22        27.88 

$`MTIF3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      186.31        17.82       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       244.50       131.21        86.96        14.30        19.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
       14.33        17.03         0.10        15.88        22.95        18.15 
TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X 
        9.14        13.58         1.38        16.31         9.63        10.26 
TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
       17.23        17.75        37.18        37.68        24.99        35.61 
TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       33.07        23.90        41.52        24.26        24.76        29.39 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A9SE 
       34.88        25.45        28.14         6.87        18.38        23.28 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        36.59         0.56        28.47        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0F 
       51.72        28.41        37.02        49.25        27.55        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  MTIF3 MUTATED MTIF3 WILD-TYPE 
          27.88            0.10 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
          40.01          244.50 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
         34.220          43.085 
[1] "27.9 - 40.0 (34.2)" "0.1 - 244.5 (43.1)"
[1] "hr="     "9300000"
D46V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTIF3 MUTATED    2       0        1        0        0         0         0
  MTIF3 WILD-TYPE 44      18       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MTIF3 MUTATED           0         0          0          0          0
  MTIF3 WILD-TYPE         1         2          1          6          5
D46V3, multiclass
            clus
vv           MTIF3 MUTATED MTIF3 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  MTIF3 MUTATED    3  0  0
  MTIF3 WILD-TYPE 71 50  6
D46V4, multiclass
    clus
vv   MTIF3 MUTATED MTIF3 WILD-TYPE
  T1             3              71
  T2             0              50
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  MTIF3 MUTATED    0     0
  MTIF3 WILD-TYPE 45    12
D46V5, multiclass
D46V6, binary
                 cls
clus                0   1
  MTIF3 MUTATED     3   0
  MTIF3 WILD-TYPE 110   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF3 MUTATED      3    0
  MTIF3 WILD-TYPE  110    4
   clus
vv  MTIF3 MUTATED MTIF3 WILD-TYPE
  0             3             110
  1             0               4
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  MTIF3 MUTATED     2   1
  MTIF3 WILD-TYPE 106  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF3 MUTATED      2    1
  MTIF3 WILD-TYPE  106   20
     clus
vv    MTIF3 MUTATED MTIF3 WILD-TYPE
  NO              2             106
  YES             1              20
[1] 2 2
[1] FALSE
D46V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTIF3 MUTATED       0                         0     2
  MTIF3 WILD-TYPE     4                         6   114
D46V9, multiclass
[1] "Remove cluster labels:" "MTIF3 MUTATED"         
clus
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              2             124 
     TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-ZM-AA0E      TCGA-2G-AAEW 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4      TCGA-2G-AAF6 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH      TCGA-2G-AAFI 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM      TCGA-2G-AAFN 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY      TCGA-2G-AAFZ 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGT      TCGA-2G-AAGV 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGW      TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAH0      TCGA-2G-AAH2      TCGA-2G-AAH3      TCGA-2G-AAH4 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAH8      TCGA-2G-AAHA      TCGA-2G-AAHC      TCGA-2G-AAHG 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAKD      TCGA-2G-AAKG      TCGA-2G-AAKH      TCGA-2G-AAKL 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAKM      TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-2G-AALP 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2X-A9D5      TCGA-2X-A9D6      TCGA-4K-AA1G      TCGA-4K-AA1H 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-S6-A8JW      TCGA-S6-A8JX 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-S6-A8JY      TCGA-SB-A6J6      TCGA-SB-A76C      TCGA-SN-A6IS 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-SN-A84W      TCGA-SN-A84X      TCGA-SN-A84Y      TCGA-SO-A8JP 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-VF-A8A8      TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-VF-A8AC 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-VF-A8AD      TCGA-VF-A8AE      TCGA-W4-A7U2      TCGA-W4-A7U4 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-WZ-A7V3      TCGA-WZ-A7V4      TCGA-WZ-A7V5      TCGA-WZ-A8D5 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-X3-A8G4      TCGA-XE-A8H1      TCGA-XE-A8H4      TCGA-XE-A9SE 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AANJ      TCGA-XE-AANR      TCGA-XE-AAO3      TCGA-XE-AAO4 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AAO6      TCGA-XE-AAOB      TCGA-XE-AAOC      TCGA-XE-AAOD 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AAOF      TCGA-XE-AAOJ      TCGA-XE-AAOL      TCGA-XY-A89B 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XY-A8S2      TCGA-XY-A8S3      TCGA-XY-A9T9      TCGA-YU-A90P 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-YU-A90S      TCGA-YU-A90W      TCGA-YU-A90Y      TCGA-YU-A912 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-YU-AA4L      TCGA-YU-AA61      TCGA-ZM-AA05      TCGA-ZM-AA06 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-ZM-AA0B      TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
D46V10, binary
                 cls
clus                0   1
  MTIF3 MUTATED     1   2
  MTIF3 WILD-TYPE  11 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF3 MUTATED      1    2
  MTIF3 WILD-TYPE   11  107
                        clus
vv                       MTIF3 MUTATED MTIF3 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(47) Variable = BTN2A2 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  BTN2A2 MUTATED     3   0
  BTN2A2 WILD-TYPE 124   4
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              128 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               0                4 
$`BTN2A2 MUTATED`
TCGA-2G-AAGP TCGA-SB-A76C TCGA-VF-A8AC 
      132.10         1.38        35.61 

$`BTN2A2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
       17.82       208.44       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
       13.58        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        37.68        24.99        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
            1.38             0.10 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
           132.1            244.5 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
          35.610           41.605 
[1] "1.4 - 132.1 (35.6)" "0.1 - 244.5 (41.6)"
[1] "hr="     "9200000"
D47V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTN2A2 MUTATED    0       0        1        0        0         1         0
  BTN2A2 WILD-TYPE 46      18       24       11        4         4         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BTN2A2 MUTATED           0         0          0          0          0
  BTN2A2 WILD-TYPE         1         2          1          6          5
D47V3, multiclass
[1] "Remove cluster labels:" "BTN2A2 MUTATED"        
clus
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               2              123 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEW 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGS 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGT       TCGA-2G-AAGW       TCGA-2G-AAGX       TCGA-2G-AAGY 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGZ       TCGA-2G-AAH0       TCGA-2G-AAH2       TCGA-2G-AAH3 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAH4       TCGA-2G-AAH8       TCGA-2G-AAHA       TCGA-2G-AAHC 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG       TCGA-2G-AAKH 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5       TCGA-2G-AAL7 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6       TCGA-4K-AA1G 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-S6-A8JW 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-S6-A8JX       TCGA-S6-A8JY       TCGA-SB-A6J6       TCGA-SN-A6IS 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-SN-A84W       TCGA-SN-A84X       TCGA-SN-A84Y       TCGA-SO-A8JP 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-VF-A8AD 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-VF-A8AE       TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-X3-A8G4       TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-A9SE       TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AANV       TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AAOB       TCGA-XE-AAOC       TCGA-XE-AAOD       TCGA-XE-AAOF 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AAOJ       TCGA-XE-AAOL       TCGA-XY-A89B       TCGA-XY-A8S2 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XY-A8S3       TCGA-XY-A9T9       TCGA-YU-A90P       TCGA-YU-A90Q 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-YU-A90S       TCGA-YU-A90W       TCGA-YU-A90Y       TCGA-YU-A912 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-YU-A94D       TCGA-YU-A94I       TCGA-YU-AA4L       TCGA-YU-AA61 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B       TCGA-ZM-AA0D 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
                  vv
clus               T1 T2 T3
  BTN2A2 MUTATED    2  1  0
  BTN2A2 WILD-TYPE 72 49  6
D47V4, multiclass
    clus
vv   BTN2A2 MUTATED BTN2A2 WILD-TYPE
  T1              2               72
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  BTN2A2 MUTATED    0     1
  BTN2A2 WILD-TYPE 45    11
D47V5, multiclass
[1] "Remove cluster labels:" "BTN2A2 MUTATED"        
clus
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               1               56 
      TCGA-2G-AAG0       TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFY       TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGJ       TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGO       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
D47V6, binary
                  cls
clus                 0   1
  BTN2A2 MUTATED     3   0
  BTN2A2 WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      3    0
  BTN2A2 WILD-TYPE  110    4
   clus
vv  BTN2A2 MUTATED BTN2A2 WILD-TYPE
  0              3              110
  1              0                4
[1] 2 2
[1] FALSE
D47V7, binary
                  cls
clus                 0   1
  BTN2A2 MUTATED     3   0
  BTN2A2 WILD-TYPE 105  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      3    0
  BTN2A2 WILD-TYPE  105   21
     clus
vv    BTN2A2 MUTATED BTN2A2 WILD-TYPE
  NO               3              105
  YES              0               21
[1] 2 2
[1] FALSE
D47V8, continuous
[1] "Remove cluster labels:" "BTN2A2 MUTATED"        
clus
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               2               99 
      TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-ZM-AA0E       TCGA-2G-AAEX 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6       TCGA-2G-AAF8 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI       TCGA-2G-AAFJ 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN       TCGA-2G-AAFO 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAFZ       TCGA-2G-AAG5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGS 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW       TCGA-2G-AAGX 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0       TCGA-2G-AAH2 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8       TCGA-2G-AAHA 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AAAL       TCGA-S6-A8JW 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-S6-A8JX       TCGA-SB-A6J6       TCGA-SN-A84Y       TCGA-SO-A8JP 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5       TCGA-WZ-A8D5 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5       TCGA-XE-A9SE 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR       TCGA-XE-AANV 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6       TCGA-XE-AAOC 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ       TCGA-XE-AAOL 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B       TCGA-ZM-AA0D 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTN2A2 MUTATED       0                         0     3
  BTN2A2 WILD-TYPE     4                         6   113
D47V9, multiclass
                           clus
vv                          BTN2A2 MUTATED BTN2A2 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D47V10, binary
                  cls
clus                 0   1
  BTN2A2 MUTATED     0   3
  BTN2A2 WILD-TYPE  12 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      0    3
  BTN2A2 WILD-TYPE   12  106
                        clus
vv                       BTN2A2 MUTATED BTN2A2 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(48) Variable = RUNX2 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  RUNX2 MUTATED     4   0
  RUNX2 WILD-TYPE 123   4
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             127 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              0               4 
$`RUNX2 MUTATED`
TCGA-2G-AAG3 TCGA-2G-AAGW TCGA-SB-A6J6 TCGA-YU-A912 
       52.37       161.06        13.58        28.47 

$`RUNX2 WILD-TYPE`
TCGA-2G-AAG0 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       80.19        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      158.33       144.85       148.83       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C 
        0.10        15.88        22.95        18.15         9.14         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
       16.31         9.63        10.26        17.23        17.75        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        55.92        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B 
        8.88        67.66        41.69        50.96         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       22.09        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       36.59         0.56        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
          13.58            0.10 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
         161.06          244.50 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          40.42           41.52 
[1] "13.6 - 161.1 (40.4)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "2.5e+07"
D48V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUNX2 MUTATED    2       0        1        0        0         0         0
  RUNX2 WILD-TYPE 44      18       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RUNX2 MUTATED           0         0          0          0          1
  RUNX2 WILD-TYPE         1         2          1          6          4
D48V3, multiclass
            clus
vv           RUNX2 MUTATED RUNX2 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             1               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              T1 T2 T3
  RUNX2 MUTATED    3  1  0
  RUNX2 WILD-TYPE 71 49  6
D48V4, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  T1             3              71
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  RUNX2 MUTATED    1     0
  RUNX2 WILD-TYPE 44    12
D48V5, multiclass
[1] "Remove cluster labels:" "RUNX2 MUTATED"         
clus
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              1              56 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAFM      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAFY      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGX 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-4K-AA1H      TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-VF-A8A8      TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
D48V6, binary
                 cls
clus                0   1
  RUNX2 MUTATED     3   0
  RUNX2 WILD-TYPE 110   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      3    0
  RUNX2 WILD-TYPE  110    4
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             3             110
  1             0               4
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  RUNX2 MUTATED     4   0
  RUNX2 WILD-TYPE 104  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      4    0
  RUNX2 WILD-TYPE  104   21
     clus
vv    RUNX2 MUTATED RUNX2 WILD-TYPE
  NO              4             104
  YES             0              21
[1] 2 2
[1] FALSE
D48V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX2 MUTATED       0                         1     3
  RUNX2 WILD-TYPE     4                         5   113
D48V9, multiclass
                           clus
vv                          RUNX2 MUTATED RUNX2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 3             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"
D48V10, binary
                 cls
clus                0   1
  RUNX2 MUTATED     0   3
  RUNX2 WILD-TYPE  12 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      0    3
  RUNX2 WILD-TYPE   12  106
                        clus
vv                       RUNX2 MUTATED RUNX2 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(49) Variable = SSBP3 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  SSBP3 MUTATED     3   0
  SSBP3 WILD-TYPE 124   4
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             128 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              0               4 
$`SSBP3 MUTATED`
TCGA-2G-AAFM TCGA-2G-AAFV TCGA-YU-A90P 
       16.54        45.67        68.02 

$`SSBP3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ 
       26.04        24.66        25.41        22.52        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
       15.48        22.09        27.72         9.24        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  SSBP3 MUTATED SSBP3 WILD-TYPE 
          16.54            0.10 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          68.02          244.50 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
         45.670          41.455 
[1] "16.5 - 68.0 (45.7)" "0.1 - 244.5 (41.5)"
[1] "hr="     "9200000"
D49V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SSBP3 MUTATED    1       0        1        0        0         1         0
  SSBP3 WILD-TYPE 45      18       24       11        4         4         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SSBP3 MUTATED           0         0          0          0          0
  SSBP3 WILD-TYPE         1         2          1          6          5
D49V3, multiclass
            clus
vv           SSBP3 MUTATED SSBP3 WILD-TYPE
  IS                     1              45
  STAGE I                0              18
  STAGE IA               1              24
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              1               4
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             0               5
[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              T1 T2 T3
  SSBP3 MUTATED    2  1  0
  SSBP3 WILD-TYPE 72 49  6
D49V4, multiclass
    clus
vv   SSBP3 MUTATED SSBP3 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  SSBP3 MUTATED    1     1
  SSBP3 WILD-TYPE 44    11
D49V5, multiclass
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              2              55 
     TCGA-2G-AAG0      TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFY      TCGA-2G-AAG5 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8      TCGA-2G-AAG9 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE      TCGA-2G-AAGF 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGW      TCGA-2G-AAGX      TCGA-2G-AAGY 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGZ      TCGA-2G-AAH2      TCGA-2G-AAHG      TCGA-2G-AAHL 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKG 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-4K-AA1G      TCGA-4K-AA1H 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-4K-AA1I      TCGA-4K-AAAL      TCGA-SO-A8JP      TCGA-VF-A8A8 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-X3-A8G4 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
D49V6, binary
                 cls
clus                0   1
  SSBP3 MUTATED     2   0
  SSBP3 WILD-TYPE 111   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    0
  SSBP3 WILD-TYPE  111    4
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             2             111
  1             0               4
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  SSBP3 MUTATED     3   0
  SSBP3 WILD-TYPE 105  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      3    0
  SSBP3 WILD-TYPE  105   21
     clus
vv    SSBP3 MUTATED SSBP3 WILD-TYPE
  NO              3             105
  YES             0              21
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              2              99 
     TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-ZM-AA0E      TCGA-2G-AAEX 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAF1      TCGA-2G-AAF4      TCGA-2G-AAF6      TCGA-2G-AAF8 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFG      TCGA-2G-AAFH      TCGA-2G-AAFI      TCGA-2G-AAFJ 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFL      TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFY 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFZ      TCGA-2G-AAG5      TCGA-2G-AAG6      TCGA-2G-AAG7 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAG8      TCGA-2G-AAG9      TCGA-2G-AAGA      TCGA-2G-AAGC 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGE      TCGA-2G-AAGF      TCGA-2G-AAGG      TCGA-2G-AAGI 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGJ      TCGA-2G-AAGK      TCGA-2G-AAGM      TCGA-2G-AAGN 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGO      TCGA-2G-AAGP      TCGA-2G-AAGS      TCGA-2G-AAGT 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGV      TCGA-2G-AAGW      TCGA-2G-AAGX      TCGA-2G-AAGY 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAGZ      TCGA-2G-AAH0      TCGA-2G-AAH2      TCGA-2G-AAH3 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAH4      TCGA-2G-AAH8      TCGA-2G-AAHA      TCGA-2G-AAHC 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAHG      TCGA-2G-AAHL      TCGA-2G-AAHN      TCGA-2G-AAHP 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAHT      TCGA-2G-AAKD      TCGA-2G-AAKG      TCGA-2G-AAKH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAKL      TCGA-2G-AAKM      TCGA-2G-AAL5      TCGA-2G-AAL7 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AALP      TCGA-2X-A9D5      TCGA-2X-A9D6      TCGA-4K-AA1G 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-4K-AA1H      TCGA-4K-AAAL      TCGA-S6-A8JW      TCGA-S6-A8JX 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-SB-A6J6      TCGA-SB-A76C      TCGA-SN-A84Y      TCGA-SO-A8JP 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-WZ-A7V3      TCGA-WZ-A7V4      TCGA-WZ-A7V5      TCGA-WZ-A8D5 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XE-A8H1      TCGA-XE-A8H4      TCGA-XE-A8H5      TCGA-XE-A9SE 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XE-AANI      TCGA-XE-AANJ      TCGA-XE-AANR      TCGA-XE-AANV 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XE-AAO3      TCGA-XE-AAO4      TCGA-XE-AAO6      TCGA-XE-AAOC 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XE-AAOD      TCGA-XE-AAOF      TCGA-XE-AAOJ      TCGA-XE-AAOL 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-ZM-AA05      TCGA-ZM-AA06      TCGA-ZM-AA0B      TCGA-ZM-AA0D 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSBP3 MUTATED       0                         0     3
  SSBP3 WILD-TYPE     4                         6   113
D49V9, multiclass
                           clus
vv                          SSBP3 MUTATED SSBP3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D49V10, binary
                 cls
clus                0   1
  SSBP3 MUTATED     0   2
  SSBP3 WILD-TYPE  12 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      0    2
  SSBP3 WILD-TYPE   12  107
                        clus
vv                       SSBP3 MUTATED SSBP3 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(50) Variable = SP4 MUTATION ANALYSIS
D50V1, survival
               sevent
clus2             0   1
  SP4 MUTATED     3   0
  SP4 WILD-TYPE 124   4
  SP4 MUTATED SP4 WILD-TYPE 
            3           128 
  SP4 MUTATED SP4 WILD-TYPE 
            0             4 
$`SP4 MUTATED`
TCGA-2G-AAGA TCGA-2G-AAKG TCGA-XY-A8S2 
       80.19       216.92        22.09 

$`SP4 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       73.45        84.99        81.47        89.88        85.84       103.13 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       96.59       119.05       127.92       120.20       132.36       132.10 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
      158.33       144.85       148.83       161.06       181.28       175.20 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
      172.04       180.07       199.23        59.90       204.16        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
      110.10       182.10        59.80       232.80       211.89       186.31 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
       17.82       208.44       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
       37.18        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       41.52        24.26        24.76        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       15.48        27.72         9.24        68.02        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       36.59         0.56        28.47        71.24        17.62        51.72 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.41        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  SP4 MUTATED SP4 WILD-TYPE 
        22.09          0.10 
  SP4 MUTATED SP4 WILD-TYPE 
       216.92        244.50 
  SP4 MUTATED SP4 WILD-TYPE 
       80.190        41.455 
[1] "22.1 - 216.9 (80.2)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9300000"
D50V2, continuous
               vv
clus            IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP4 MUTATED    0       2        0        0        0         1         0
  SP4 WILD-TYPE 46      16       25       11        4         4         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SP4 MUTATED           0         0          0          0          0
  SP4 WILD-TYPE         1         2          1          6          5
D50V3, multiclass
            clus
vv           SP4 MUTATED SP4 WILD-TYPE
  IS                   0            46
  STAGE I              2            16
  STAGE IA             0            25
  STAGE IB             0            11
  STAGE II             0             4
  STAGE IIA            1             4
  STAGE IIB            0             1
  STAGE IIC            0             1
  STAGE III            0             2
  STAGE IIIA           0             1
  STAGE IIIB           0             6
  STAGE IIIC           0             5
[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            T1 T2 T3
  SP4 MUTATED    2  1  0
  SP4 WILD-TYPE 72 49  6
D50V4, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  T1           2            72
  T2           1            49
  T3           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1+N2
  SP4 MUTATED    1     1
  SP4 WILD-TYPE 44    11
D50V5, multiclass
[1] "Remove cluster labels:" "SP4 MUTATED"           
clus
  SP4 MUTATED SP4 WILD-TYPE 
            2            55 
   TCGA-2G-AAG0    TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAF6    TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFI 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFJ    TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFV    TCGA-2G-AAFY    TCGA-2G-AAG5    TCGA-2G-AAG6    TCGA-2G-AAG7 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAG8    TCGA-2G-AAG9    TCGA-2G-AAGC    TCGA-2G-AAGE    TCGA-2G-AAGF 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGG    TCGA-2G-AAGI    TCGA-2G-AAGJ    TCGA-2G-AAGK    TCGA-2G-AAGM 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGN    TCGA-2G-AAGO    TCGA-2G-AAGP    TCGA-2G-AAGS    TCGA-2G-AAGW 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGX    TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH2    TCGA-2G-AAHG 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT    TCGA-2G-AAL5 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAL7    TCGA-4K-AA1G    TCGA-4K-AA1H    TCGA-4K-AA1I    TCGA-4K-AAAL 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-SO-A8JP    TCGA-VF-A8A8    TCGA-VF-A8AA    TCGA-VF-A8AB    TCGA-X3-A8G4 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
D50V6, binary
               cls
clus              0   1
  SP4 MUTATED     3   0
  SP4 WILD-TYPE 110   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      3    0
  SP4 WILD-TYPE  110    4
   clus
vv  SP4 MUTATED SP4 WILD-TYPE
  0           3           110
  1           0             4
[1] 2 2
[1] FALSE
D50V7, binary
               cls
clus              0   1
  SP4 MUTATED     3   0
  SP4 WILD-TYPE 105  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      3    0
  SP4 WILD-TYPE  105   21
     clus
vv    SP4 MUTATED SP4 WILD-TYPE
  NO            3           105
  YES           0            21
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "SP4 MUTATED"           
clus
  SP4 MUTATED SP4 WILD-TYPE 
            2            99 
   TCGA-2G-AAG0    TCGA-2G-AAG3    TCGA-ZM-AA0E    TCGA-2G-AAEX    TCGA-2G-AAF1 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAF4    TCGA-2G-AAF6    TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFI    TCGA-2G-AAFJ    TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFO    TCGA-2G-AAFV    TCGA-2G-AAFY    TCGA-2G-AAFZ    TCGA-2G-AAG5 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAG6    TCGA-2G-AAG7    TCGA-2G-AAG8    TCGA-2G-AAG9    TCGA-2G-AAGC 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGE    TCGA-2G-AAGF    TCGA-2G-AAGG    TCGA-2G-AAGI    TCGA-2G-AAGJ 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGK    TCGA-2G-AAGM    TCGA-2G-AAGN    TCGA-2G-AAGO    TCGA-2G-AAGP 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGS    TCGA-2G-AAGT    TCGA-2G-AAGV    TCGA-2G-AAGW    TCGA-2G-AAGX 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH0    TCGA-2G-AAH2    TCGA-2G-AAH3 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAH4    TCGA-2G-AAH8    TCGA-2G-AAHA    TCGA-2G-AAHC    TCGA-2G-AAHG 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT    TCGA-2G-AAKD 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAKH    TCGA-2G-AAKL    TCGA-2G-AAKM    TCGA-2G-AAL5    TCGA-2G-AAL7 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AALP    TCGA-2X-A9D5    TCGA-2X-A9D6    TCGA-4K-AA1G    TCGA-4K-AA1H 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-4K-AAAL    TCGA-S6-A8JW    TCGA-S6-A8JX    TCGA-SB-A6J6    TCGA-SB-A76C 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-SN-A84Y    TCGA-SO-A8JP    TCGA-WZ-A7V3    TCGA-WZ-A7V4    TCGA-WZ-A7V5 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-WZ-A8D5    TCGA-XE-A8H1    TCGA-XE-A8H4    TCGA-XE-A8H5    TCGA-XE-A9SE 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-XE-AANI    TCGA-XE-AANJ    TCGA-XE-AANR    TCGA-XE-AANV    TCGA-XE-AAO3 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-XE-AAO4    TCGA-XE-AAO6    TCGA-XE-AAOC    TCGA-XE-AAOD    TCGA-XE-AAOF 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-XE-AAOJ    TCGA-XE-AAOL    TCGA-ZM-AA05    TCGA-ZM-AA06    TCGA-ZM-AA0B 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-ZM-AA0D    TCGA-ZM-AA0F    TCGA-ZM-AA0H    TCGA-ZM-AA0N 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP4 MUTATED       0                         0     3
  SP4 WILD-TYPE     4                         6   113
D50V9, multiclass
                           clus
vv                          SP4 MUTATED SP4 WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D50V10, binary
               cls
clus              0   1
  SP4 MUTATED     0   3
  SP4 WILD-TYPE  12 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      0    3
  SP4 WILD-TYPE   12  106
                        clus
vv                       SP4 MUTATED SP4 WILD-TYPE
  HISPANIC OR LATINO               0            12
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(51) Variable = PCMTD1 MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2                0   1
  PCMTD1 MUTATED     5   0
  PCMTD1 WILD-TYPE 122   4
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              126 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               0                4 
$`PCMTD1 MUTATED`
TCGA-ZM-AA0E TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAGJ TCGA-2G-AAHP 
       26.66        76.11        45.21        96.59       186.31 

$`PCMTD1 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 
       50.27        52.37        20.32        41.39        46.13       114.77 
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      128.58       203.28        22.19        26.04        24.66        16.54 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 
       25.41        22.52        45.67        36.13        44.48        75.58 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       73.35        81.37        75.25        73.45        80.19        84.99 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       81.47        89.88        85.84       103.13       119.05       127.92 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      120.20       132.36       132.10       158.33       144.85       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      161.06       181.28       175.20       172.04       180.07       199.23 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       204.16        73.91       110.10       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      232.80       211.89        17.82       208.44       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      230.89       229.22       244.50       131.21        86.96        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
       19.96        14.33        17.03         0.10        15.88        22.95 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       18.15         9.14        13.58         1.38        16.31         9.63 
TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB 
       10.26        17.23        17.75        37.18        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V3 
       35.61        33.07        23.90        41.52        24.26        24.76 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
       29.39        34.88        25.45        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       40.01        23.28        34.22        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       93.93        12.07         7.89        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       41.69        50.96         0.43        15.48        22.09        27.72 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        9.24        68.02        64.57        31.92        36.59         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
       28.47        71.24        17.62        51.72        28.41        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       49.25        27.55        27.88        22.39        57.07        20.84 

  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           26.66             0.10 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
          186.31           244.50 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           76.11            40.70 
[1] "26.7 - 186.3 (76.1)" "0.1 - 244.5 (40.7)" 
[1] "hr="     "2.6e+07"
D51V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCMTD1 MUTATED    1       1        2        0        0         0         1
  PCMTD1 WILD-TYPE 45      17       23       11        4         5         0
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PCMTD1 MUTATED           0         0          0          0          0
  PCMTD1 WILD-TYPE         1         2          1          6          5
D51V3, multiclass
            clus
vv           PCMTD1 MUTATED PCMTD1 WILD-TYPE
  IS                      1               45
  STAGE I                 1               17
  STAGE IA                2               23
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               1                0
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  PCMTD1 MUTATED    4  1  0
  PCMTD1 WILD-TYPE 70 49  6
D51V4, multiclass
    clus
vv   PCMTD1 MUTATED PCMTD1 WILD-TYPE
  T1              4               70
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PCMTD1 MUTATED    3     1
  PCMTD1 WILD-TYPE 42    11
D51V5, multiclass
       clus
vv      PCMTD1 MUTATED PCMTD1 WILD-TYPE
  N0                 3               42
  N1+N2              1               11
[1] 2 2
[1] FALSE
D51V6, binary
                  cls
clus                 0   1
  PCMTD1 MUTATED     5   0
  PCMTD1 WILD-TYPE 108   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      5    0
  PCMTD1 WILD-TYPE  108    4
   clus
vv  PCMTD1 MUTATED PCMTD1 WILD-TYPE
  0              5              108
  1              0                4
[1] 2 2
[1] FALSE
D51V7, binary
                  cls
clus                 0   1
  PCMTD1 MUTATED     3   2
  PCMTD1 WILD-TYPE 105  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      3    2
  PCMTD1 WILD-TYPE  105   19
     clus
vv    PCMTD1 MUTATED PCMTD1 WILD-TYPE
  NO               3              105
  YES              2               19
[1] 2 2
[1] FALSE
D51V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCMTD1 MUTATED       0                         1     4
  PCMTD1 WILD-TYPE     4                         5   112
D51V9, multiclass
                           clus
vv                          PCMTD1 MUTATED PCMTD1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                  4              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"
D51V10, binary
                  cls
clus                 0   1
  PCMTD1 MUTATED     0   5
  PCMTD1 WILD-TYPE  12 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      0    5
  PCMTD1 WILD-TYPE   12  104
                        clus
vv                       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              5              104
[1] 2 2
[1] FALSE

Clustering(52) Variable = RBM3 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  RBM3 MUTATED     3   0
  RBM3 WILD-TYPE 124   4
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            128 
  RBM3 MUTATED RBM3 WILD-TYPE 
             0              4 
$`RBM3 MUTATED`
TCGA-2G-AAKD TCGA-WZ-A7V3 TCGA-ZM-AA06 
      208.44        24.76        49.25 

$`RBM3 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 
       50.27        52.37        26.66        20.32        41.39        46.13 
TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       76.11       114.77       128.58       203.28        45.21        22.19 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       26.04        24.66        16.54        25.41        22.52        45.67 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 
       36.13        44.48        75.58        73.35        81.37        75.25 
TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       73.45        80.19        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
      103.13        96.59       119.05       127.92       120.20       132.36 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      132.10       158.33       144.85       148.83       161.06       181.28 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
      175.20       172.04       180.07       199.23        59.90       204.16 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN 
       73.91       110.10       182.10        59.80       232.80       211.89 
TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
      186.31        17.82       216.92       225.60       230.89       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      244.50       131.21        86.96        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y 
       13.58         1.38        16.31         9.63        10.26        17.23 
TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD 
       17.75        37.18        37.68        24.99        35.61        33.07 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       23.90        41.52        24.26        29.39        34.88        25.45 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI 
       28.14         6.87        18.38        40.01        23.28        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL 
       16.87         8.88        67.66        41.69        50.96         0.43 
TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
       15.48        22.09        27.72         9.24        68.02        64.57 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        36.59         0.56        28.47        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       51.72        28.41        37.02        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

  RBM3 MUTATED RBM3 WILD-TYPE 
         24.76           0.10 
  RBM3 MUTATED RBM3 WILD-TYPE 
        208.44         244.50 
  RBM3 MUTATED RBM3 WILD-TYPE 
        49.250         41.455 
[1] "24.8 - 208.4 (49.2)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "9300000"
D52V2, continuous
                vv
clus             IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM3 MUTATED    0       1        0        1        0         0         0
  RBM3 WILD-TYPE 46      17       25       10        4         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RBM3 MUTATED           0         1          0          0          0
  RBM3 WILD-TYPE         1         1          1          6          5
D52V3, multiclass
            clus
vv           RBM3 MUTATED RBM3 WILD-TYPE
  IS                    0             46
  STAGE I               1             17
  STAGE IA              0             25
  STAGE IB              1             10
  STAGE II              0              4
  STAGE IIA             0              5
  STAGE IIB             0              1
  STAGE IIC             0              1
  STAGE III             1              1
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
[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             T1 T2 T3
  RBM3 MUTATED    1  2  0
  RBM3 WILD-TYPE 73 48  6
D52V4, multiclass
    clus
vv   RBM3 MUTATED RBM3 WILD-TYPE
  T1            1             73
  T2            2             48
  T3            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  RBM3 MUTATED    0     0
  RBM3 WILD-TYPE 45    12
D52V5, multiclass
D52V6, binary
                cls
clus               0   1
  RBM3 MUTATED     2   0
  RBM3 WILD-TYPE 111   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM3 MUTATED      2    0
  RBM3 WILD-TYPE  111    4
   clus
vv  RBM3 MUTATED RBM3 WILD-TYPE
  0            2            111
  1            0              4
[1] 2 2
[1] FALSE
D52V7, binary
                cls
clus               0   1
  RBM3 MUTATED     3   0
  RBM3 WILD-TYPE 105  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM3 MUTATED      3    0
  RBM3 WILD-TYPE  105   21
     clus
vv    RBM3 MUTATED RBM3 WILD-TYPE
  NO             3            105
  YES            0             21
[1] 2 2
[1] FALSE
D52V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM3 MUTATED       0                         0     3
  RBM3 WILD-TYPE     4                         6   113
D52V9, multiclass
                           clus
vv                          RBM3 MUTATED RBM3 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            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"
D52V10, binary
                cls
clus               0   1
  RBM3 MUTATED     0   3
  RBM3 WILD-TYPE  12 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM3 MUTATED      0    3
  RBM3 WILD-TYPE   12  106
                        clus
vv                       RBM3 MUTATED RBM3 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3            106
[1] 2 2
[1] FALSE

Clustering(53) Variable = ZNF814 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED     4   0
  ZNF814 WILD-TYPE 123   4
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               4              127 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               0                4 
$`ZNF814 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF8 TCGA-VF-A8A8 TCGA-XE-AAO3 
       41.39       128.58        37.18        93.93 

$`ZNF814 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        20.32        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL 
      114.77       203.28        45.21        22.19        26.04        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ 
       16.54        25.41        22.52        45.67        36.13        44.48 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       75.58        73.35        81.37        75.25        73.45        80.19 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       84.99        81.47        89.88        85.84       103.13        96.59 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      119.05       127.92       120.20       132.36       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      144.85       148.83       161.06       181.28       175.20       172.04 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
      180.07       199.23        59.90       204.16        73.91       110.10 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
      182.10        59.80       232.80       211.89       186.31        17.82 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      208.44       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        86.96        14.30        19.96        14.33        17.03 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10        15.88        22.95        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP 
        1.38        16.31         9.63        10.26        17.23        17.75 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 
       37.68        24.99        35.61        33.07        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       24.26        24.76        29.39        34.88        25.45        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ 
        6.87        18.38        40.01        23.28        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
        0.46        55.92        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
           37.18             0.10 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          128.58           244.50 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           67.66            41.52 
[1] "37.2 - 128.6 (67.7)" "0.1 - 244.5 (41.5)" 
[1] "hr="     "2.6e+07"
D53V2, continuous
                  vv
clus               IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF814 MUTATED    1       1        2        0        0         0         0
  ZNF814 WILD-TYPE 45      17       23       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZNF814 MUTATED           0         0          0          0          0
  ZNF814 WILD-TYPE         1         2          1          6          5
D53V3, multiclass
            clus
vv           ZNF814 MUTATED ZNF814 WILD-TYPE
  IS                      1               45
  STAGE I                 1               17
  STAGE IA                2               23
  STAGE IB                0               11
  STAGE II                0                4
  STAGE IIA               0                5
  STAGE IIB               0                1
  STAGE IIC               0                1
  STAGE III               0                2
  STAGE IIIA              0                1
  STAGE IIIB              0                6
  STAGE IIIC              0                5
[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               T1 T2 T3
  ZNF814 MUTATED    3  1  0
  ZNF814 WILD-TYPE 71 49  6
D53V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              3               71
  T2              1               49
  T3              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  ZNF814 MUTATED    3     0
  ZNF814 WILD-TYPE 42    12
D53V5, multiclass
       clus
vv      ZNF814 MUTATED ZNF814 WILD-TYPE
  N0                 3               42
  N1+N2              0               12
[1] 2 2
[1] FALSE
D53V6, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     4   0
  ZNF814 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      4    0
  ZNF814 WILD-TYPE  109    4
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              4              109
  1              0                4
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     2   2
  ZNF814 WILD-TYPE 106  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      2    2
  ZNF814 WILD-TYPE  106   19
     clus
vv    ZNF814 MUTATED ZNF814 WILD-TYPE
  NO               2              106
  YES              2               19
[1] 2 2
[1] FALSE
D53V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED       1                         0     3
  ZNF814 WILD-TYPE     3                         6   113
D53V9, multiclass
                           clus
vv                          ZNF814 MUTATED ZNF814 WILD-TYPE
  ASIAN                                  1                3
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D53V10, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0   4
  ZNF814 WILD-TYPE  12 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0    4
  ZNF814 WILD-TYPE   12  105
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4              105
[1] 2 2
[1] FALSE

Clustering(54) Variable = TTC38 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  TTC38 MUTATED     4   0
  TTC38 WILD-TYPE 123   4
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             127 
  TTC38 MUTATED TTC38 WILD-TYPE 
              0               4 
$`TTC38 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAH8 
       41.39        85.84       103.13        73.91 

$`TTC38 WILD-TYPE`
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 
       50.27        52.37        26.66        20.32        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ 
      114.77       128.58       203.28        45.21        22.19        26.04 
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY 
       24.66        16.54        25.41        22.52        45.67        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       44.48        75.58        73.35        81.37        75.25        73.45 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        84.99        81.47        89.88        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      127.92       120.20       132.36       132.10       158.33       144.85 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      148.83       161.06       181.28       175.20       172.04       180.07 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
      199.23        59.90       204.16       110.10       182.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
      232.80       211.89       186.31        17.82       208.44       216.92 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      225.60       230.89       229.22       244.50       131.21        86.96 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       14.30        19.96        14.33        17.03         0.10        15.88 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       22.95        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23        17.75        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       24.99        35.61        33.07        23.90        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.76        29.39        34.88        25.45        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
       18.38        40.01        23.28        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       55.92        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
       67.66        41.69        50.96         0.43        15.48        22.09 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       27.72         9.24        68.02        64.57        31.92        36.59 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56        28.47        71.24        17.62        51.72        28.41 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        49.25        27.55        27.88        22.39        57.07 
TCGA-ZM-AA0N 
       20.84 

  TTC38 MUTATED TTC38 WILD-TYPE 
          41.39            0.10 
  TTC38 MUTATED TTC38 WILD-TYPE 
         103.13          244.50 
  TTC38 MUTATED TTC38 WILD-TYPE 
         79.875          40.010 
[1] "41.4 - 103.1 (79.9)" "0.1 - 244.5 (40.0)" 
[1] "hr="     "2.6e+07"
D54V2, continuous
                 vv
clus              IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTC38 MUTATED    2       0        0        0        0         0         0
  TTC38 WILD-TYPE 44      18       25       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TTC38 MUTATED           0         0          0          0          2
  TTC38 WILD-TYPE         1         2          1          6          3
D54V3, multiclass
            clus
vv           TTC38 MUTATED TTC38 WILD-TYPE
  IS                     2              44
  STAGE I                0              18
  STAGE IA               0              25
  STAGE IB               0              11
  STAGE II               0               4
  STAGE IIA              0               5
  STAGE IIB              0               1
  STAGE IIC              0               1
  STAGE III              0               2
  STAGE IIIA             0               1
  STAGE IIIB             0               6
  STAGE IIIC             2               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              T1 T2 T3
  TTC38 MUTATED    2  1  1
  TTC38 WILD-TYPE 72 49  5
D54V4, multiclass
    clus
vv   TTC38 MUTATED TTC38 WILD-TYPE
  T1             2              72
  T2             1              49
  T3             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  TTC38 MUTATED    2     1
  TTC38 WILD-TYPE 43    11
D54V5, multiclass
       clus
vv      TTC38 MUTATED TTC38 WILD-TYPE
  N0                2              43
  N1+N2             1              11
[1] 2 2
[1] FALSE
D54V6, binary
                 cls
clus                0   1
  TTC38 MUTATED     3   1
  TTC38 WILD-TYPE 110   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC38 MUTATED      3    1
  TTC38 WILD-TYPE  110    3
   clus
vv  TTC38 MUTATED TTC38 WILD-TYPE
  0             3             110
  1             1               3
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  TTC38 MUTATED     3   1
  TTC38 WILD-TYPE 105  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC38 MUTATED      3    1
  TTC38 WILD-TYPE  105   20
     clus
vv    TTC38 MUTATED TTC38 WILD-TYPE
  NO              3             105
  YES             1              20
[1] 2 2
[1] FALSE
D54V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTC38 MUTATED       0                         0     4
  TTC38 WILD-TYPE     4                         6   112
D54V9, multiclass
                           clus
vv                          TTC38 MUTATED TTC38 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D54V10, binary
                 cls
clus                0   1
  TTC38 MUTATED     0   4
  TTC38 WILD-TYPE  12 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC38 MUTATED      0    4
  TTC38 WILD-TYPE   12  105
                        clus
vv                       TTC38 MUTATED TTC38 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE
