[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/15092576/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/TGCT-TP/15890413/transformed.cor.cli.txt"

nPatients in clinical file=133, in cluster file=147, common to both=130
[1] "Reduce the number of clustering variables from 70 to 59."
[1]  59 130
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
           25           105 
  KIT MUTATED KIT WILD-TYPE 
           25           105 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            19            111 
  KRAS MUTATED KRAS WILD-TYPE 
            19            111 
[1] "ANKLE1 MUTATION ANALYSIS"
[1] 3
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
              11              119 
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
              11              119 
[1] "FAM104B MUTATION ANALYSIS"
[1] 3
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               124 
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               124 
[1] "DDX11 MUTATION ANALYSIS"
[1] 3
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             124 
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             124 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             6            124 
  NRAS MUTATED NRAS WILD-TYPE 
             6            124 
[1] "PNPLA4 MUTATION ANALYSIS"
[1] 3
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              125 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              125 
[1] "SERINC2 MUTATION ANALYSIS"
[1] 3
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               127 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               127 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             126 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             126 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            5           125 
  DEK MUTATED DEK WILD-TYPE 
            5           125 
[1] "ERC1 MUTATION ANALYSIS"
[1] 3
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            124 
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            124 
[1] "HSF4 MUTATION ANALYSIS"
[1] 3
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            124 
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            124 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            117 
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            117 
[1] "FANK1 MUTATION ANALYSIS"
[1] 3
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             126 
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             126 
[1] "MLLT3 MUTATION ANALYSIS"
[1] 3
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             127 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             127 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             124 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             124 
[1] "SP8 MUTATION ANALYSIS"
[1] 3
  SP8 MUTATED SP8 WILD-TYPE 
            4           126 
  SP8 MUTATED SP8 WILD-TYPE 
            4           126 
[1] "KRTAP1-1 MUTATION ANALYSIS"
[1] 3
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                127 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                127 
[1] "ANKRD11 MUTATION ANALYSIS"
[1] 3
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               125 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               125 
[1] "SPIN2A MUTATION ANALYSIS"
[1] 3
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              127 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              127 
[1] "ATXN3 MUTATION ANALYSIS"
[1] 3
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             127 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             127 
[1] "SSBP3 MUTATION ANALYSIS"
[1] 3
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             127 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             127 
[1] "KRTAP10-10 MUTATION ANALYSIS"
[1] 3
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  126 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  126 
[1] "BCL11B MUTATION ANALYSIS"
[1] 3
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              125 
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              125 
[1] "FAM101B MUTATION ANALYSIS"
[1] 3
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               126 
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               126 
[1] "PSMD11 MUTATION ANALYSIS"
[1] 3
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              126 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              126 
[1] "FAM8A1 MUTATION ANALYSIS"
[1] 3
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              127 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              127 
[1] "SPTAN1 MUTATION ANALYSIS"
[1] 3
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               3              127 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               3              127 
[1] "CRB2 MUTATION ANALYSIS"
[1] 3
  CRB2 MUTATED CRB2 WILD-TYPE 
             6            124 
  CRB2 MUTATED CRB2 WILD-TYPE 
             6            124 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             126 
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             126 
[1] "GAS2L2 MUTATION ANALYSIS"
[1] 3
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               3              127 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               3              127 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             124 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             124 
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            116 
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            116 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             126 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             126 
[1] "NAT10 MUTATION ANALYSIS"
[1] 3
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             126 
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             126 
[1] "INTS4 MUTATION ANALYSIS"
[1] 3
  INTS4 MUTATED INTS4 WILD-TYPE 
              3             127 
  INTS4 MUTATED INTS4 WILD-TYPE 
              3             127 
[1] "TTC38 MUTATION ANALYSIS"
[1] 3
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             126 
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             126 
[1] "RBM3 MUTATION ANALYSIS"
[1] 3
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            127 
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            127 
[1] "TCHH MUTATION ANALYSIS"
[1] 3
  TCHH MUTATED TCHH WILD-TYPE 
             5            125 
  TCHH MUTATED TCHH WILD-TYPE 
             5            125 
[1] "ZC3H11A MUTATION ANALYSIS"
[1] 3
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               127 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               127 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            126 
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            126 
[1] "MTIF3 MUTATION ANALYSIS"
[1] 3
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             127 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             127 
[1] "MFF MUTATION ANALYSIS"
[1] 3
  MFF MUTATED MFF WILD-TYPE 
            3           127 
  MFF MUTATED MFF WILD-TYPE 
            3           127 
[1] "PABPC3 MUTATION ANALYSIS"
[1] 3
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              127 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              127 
[1] "CUX1 MUTATION ANALYSIS"
[1] 3
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            125 
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            125 
[1] "PCMTD1 MUTATION ANALYSIS"
[1] 3
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              125 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              125 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            126 
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            126 
[1] "HTT MUTATION ANALYSIS"
[1] 3
  HTT MUTATED HTT WILD-TYPE 
            3           127 
  HTT MUTATED HTT WILD-TYPE 
            3           127 
[1] "AHDC1 MUTATION ANALYSIS"
[1] 3
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             127 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             127 
[1] "RFC3 MUTATION ANALYSIS"
[1] 3
  RFC3 MUTATED RFC3 WILD-TYPE 
             3            127 
  RFC3 MUTATED RFC3 WILD-TYPE 
             3            127 
[1] "CHD4 MUTATION ANALYSIS"
[1] 3
  CHD4 MUTATED CHD4 WILD-TYPE 
             3            127 
  CHD4 MUTATED CHD4 WILD-TYPE 
             3            127 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             126 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             126 
[1] "SP4 MUTATION ANALYSIS"
[1] 3
  SP4 MUTATED SP4 WILD-TYPE 
            3           127 
  SP4 MUTATED SP4 WILD-TYPE 
            3           127 
[1] "DIAPH1 MUTATION ANALYSIS"
[1] 3
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               3              127 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               3              127 
[1] "PLEC MUTATION ANALYSIS"
[1] 3
  PLEC MUTATED PLEC WILD-TYPE 
             6            124 
  PLEC MUTATED PLEC WILD-TYPE 
             6            124 
[1] "NHS MUTATION ANALYSIS"
[1] 3
  NHS MUTATED NHS WILD-TYPE 
            3           127 
  NHS MUTATED NHS WILD-TYPE 
            3           127 
[1] "PIK3CD MUTATION ANALYSIS"
[1] 3
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              127 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              127 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             126 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             126 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            127 
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            127 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 130 columns.

[1] "Batch" "15"   
[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=124,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "129"    
freq.contrast "129"     "1"      
both >= 3     "FALSE"   "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:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B430.15.0 B430.16.0
freq.values   "1"       "129"    
freq.contrast "129"     "1"      
both >= 3     "FALSE"   "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 130 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "RACE"                 
[7] "ETHNICITY"            
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
73 50  6 
[1] "table(vv)"
vv
T1 T2 T3 
73 50  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
73 50  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
73 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
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KIT MUTATION ANALYSIS
D1V1, survival
               sevent
clus2             0   1
  KIT MUTATED    25   0
  KIT WILD-TYPE 101   4
  KIT MUTATED KIT WILD-TYPE 
           25           105 
  KIT MUTATED KIT WILD-TYPE 
            0             4 
$`KIT MUTATED`
TCGA-2G-AAF1 TCGA-2G-AAG9 TCGA-2G-AAGI TCGA-2G-AAH3 TCGA-2G-AAHA TCGA-2G-AAHL 
       38.30        63.32        92.09        59.90        98.53        59.80 
TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
       91.43         6.08         2.73         0.13         3.52         7.00 
TCGA-VF-A8AA TCGA-WZ-A7V5 TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAOF TCGA-YU-A90Q 
       37.68         0.16         0.46        53.03        41.69        54.35 
TCGA-YU-A90S TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       31.92         5.29        37.02        17.39        16.41        11.34 
TCGA-ZM-AA0H 
       46.88 

$`KIT WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC 
       71.24        72.20        61.71        63.22        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       68.38        79.76        67.96        75.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2G-AAKD 
      125.69        61.84        59.74        59.80       176.15       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       70.59         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AAO3 
        6.87        18.38        40.01        34.22        65.98        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ 
       12.07         7.89        16.87         8.88        67.66        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       21.96         0.56        58.88         7.96        40.96         8.15 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       39.35        27.55        10.85 

  KIT MUTATED KIT WILD-TYPE 
         0.13          0.10 
  KIT MUTATED KIT WILD-TYPE 
        98.53        229.22 
  KIT MUTATED KIT WILD-TYPE 
        37.02         40.01 
[1] "0.1 - 98.5 (37.0)"  "0.1 - 229.2 (40.0)"
[1] "hr="     "8.8e+07"
D1V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIT MUTATED         8        6        3        0         0         0
  KIT WILD-TYPE      11       18        8        5         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  KIT MUTATED           1         0          0          1          1        5
  KIT WILD-TYPE         0         2          1          5          4       41
D1V3, multiclass
            clus
vv           KIT MUTATED KIT WILD-TYPE
  STAGE I              8            11
  STAGE IA             6            18
  STAGE IB             3             8
  STAGE II             0             5
  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
  STAGE IS             5            41
[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 61 38  5
D1V4, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  T1          12            61
  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
D1V5, multiclass
       clus
vv      KIT MUTATED KIT WILD-TYPE
  N0              8            37
  N1+N2           1            11
[1] 2 2
[1] FALSE
D1V6, binary
               cls
clus             0  1
  KIT MUTATED   21  0
  KIT WILD-TYPE 91  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     21    0
  KIT WILD-TYPE   91    4
   clus
vv  KIT MUTATED KIT WILD-TYPE
  0          21            91
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED       2                         1    20
  KIT WILD-TYPE     2                         5    95
D1V7, multiclass
                           clus
vv                          KIT MUTATED KIT WILD-TYPE
  ASIAN                               2             2
  BLACK OR AFRICAN AMERICAN           1             5
  WHITE                              20            95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
               cls
clus             0  1
  KIT MUTATED    1 21
  KIT WILD-TYPE 10 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      1   21
  KIT WILD-TYPE   10   88
                        clus
vv                       KIT MUTATED KIT WILD-TYPE
  HISPANIC OR LATINO               1            10
  NOT HISPANIC OR LATINO          21            88
[1] 2 2
[1] FALSE

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    18   1
  KRAS WILD-TYPE 108   3
  KRAS MUTATED KRAS WILD-TYPE 
            19            111 
  KRAS MUTATED KRAS WILD-TYPE 
             1              3 
$`KRAS MUTATED`
TCGA-2G-AAEW TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAG3 TCGA-2G-AAG9 TCGA-2G-AAH8 
       20.32        59.70       102.35        52.37        63.32        61.84 
TCGA-2G-AAHA TCGA-2G-AAHP TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A76C 
       98.53       176.15         7.00         4.83        20.68         1.38 
TCGA-VF-A8AC TCGA-W4-A7U2 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XY-A9T9 
       35.61        41.52         0.82        18.38        40.01         6.90 
TCGA-ZM-AA05 
       37.02 

$`KRAS WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI 
       30.35        38.30       122.40       191.31        36.99        14.14 
TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV 
       14.56        17.16         9.57        14.86        16.50        40.70 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 
       36.13        36.89        40.01        71.24        72.20        61.71 
TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       63.22        68.22        72.85        68.38        79.76        67.96 
TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO 
       92.09        75.09       108.16        59.64       106.39       115.00 
TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX 
      120.62        59.28       124.57       128.94        61.45       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       80.94        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD 
       59.74        59.80        59.80        91.43         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-S6-A8JX 
       70.59         2.73         0.13         3.52         0.10        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-A8AD TCGA-VF-A8AE 
        3.52        37.18        37.68        24.99        33.07        23.90 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.26         3.65         5.06         0.16        28.14         6.87 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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-YU-A90P TCGA-YU-A90Q 
        0.43         8.32        12.92        20.12        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
       40.96         8.15        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  KRAS MUTATED KRAS WILD-TYPE 
          0.82           0.10 
  KRAS MUTATED KRAS WILD-TYPE 
        176.15         229.22 
  KRAS MUTATED KRAS WILD-TYPE 
         37.02          38.30 
[1] "0.8 - 176.2 (37.0)" "0.1 - 229.2 (38.3)"
[1] "hr=" "2.8"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED         1        3        1        0         0         0
  KRAS WILD-TYPE      18       21       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  KRAS MUTATED           1         0          0          1          1        8
  KRAS WILD-TYPE         0         2          1          5          4       38
D2V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               1             18
  STAGE IA              3             21
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              8             38
[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 64 42  5
D2V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            9             64
  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
D2V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0               6             39
  N1+N2            1             11
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus              0  1
  KRAS MUTATED   18  0
  KRAS WILD-TYPE 94  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     18    0
  KRAS WILD-TYPE   94    4
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           18             94
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0    18
  KRAS WILD-TYPE     4                         6    97
D2V7, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               18             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"
D2V8, binary
                cls
clus              0  1
  KRAS MUTATED    1 18
  KRAS WILD-TYPE 10 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1   18
  KRAS WILD-TYPE   10   91
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1             10
  NOT HISPANIC OR LATINO           18             91
[1] 2 2
[1] FALSE

Clustering(3) Variable = ANKLE1 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ANKLE1 MUTATED    11   0
  ANKLE1 WILD-TYPE 115   4
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
              11              119 
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
               0                4 
$`ANKLE1 MUTATED`
TCGA-2G-AAF6 TCGA-2G-AAFJ TCGA-2G-AAHP TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-2G-AAL7 
      102.35        14.56       176.15       212.65       184.41       131.21 
TCGA-S6-A8JY TCGA-VF-A8AC TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-ZM-AA06 
        9.14        35.61         0.82        40.01        39.35 

$`ANKLE1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       36.99        14.14        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH 
       59.80        59.80        91.43         6.08       122.50       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
       95.67       229.22        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 
        7.00         0.10         4.83        20.68        18.15        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         3.52 
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-X3-A8G4 TCGA-XE-A8H1 
       24.26         3.65         5.06         0.16        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       18.38        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B 
       58.88         7.96        40.96         8.15        37.02        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
            0.82             0.10 
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
          212.65           229.22 
  ANKLE1 MUTATED ANKLE1 WILD-TYPE 
           40.01            37.18 
[1] "0.8 - 212.7 (40.0)" "0.1 - 229.2 (37.2)"
[1] "hr="     "7.6e+07"
D3V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKLE1 MUTATED         3        1        1        0         0         0
  ANKLE1 WILD-TYPE      16       23       10        5         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ANKLE1 MUTATED           0         0          0          0          0
  ANKLE1 WILD-TYPE         1         2          1          6          5
                  vv
clus               STAGE IS
  ANKLE1 MUTATED          5
  ANKLE1 WILD-TYPE       41
D3V3, multiclass
            clus
vv           ANKLE1 MUTATED ANKLE1 WILD-TYPE
  STAGE I                 3               16
  STAGE IA                1               23
  STAGE IB                1               10
  STAGE II                0                5
  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
  STAGE IS                5               41
[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
  ANKLE1 MUTATED    7  3  1
  ANKLE1 WILD-TYPE 66 47  5
D3V4, multiclass
    clus
vv   ANKLE1 MUTATED ANKLE1 WILD-TYPE
  T1              7               66
  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
  ANKLE1 MUTATED    6     0
  ANKLE1 WILD-TYPE 39    12
D3V5, multiclass
       clus
vv      ANKLE1 MUTATED ANKLE1 WILD-TYPE
  N0                 6               39
  N1+N2              0               12
[1] 2 2
[1] FALSE
D3V6, binary
                  cls
clus                 0   1
  ANKLE1 MUTATED    11   0
  ANKLE1 WILD-TYPE 101   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKLE1 MUTATED     11    0
  ANKLE1 WILD-TYPE  101    4
   clus
vv  ANKLE1 MUTATED ANKLE1 WILD-TYPE
  0             11              101
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKLE1 MUTATED       1                         0     9
  ANKLE1 WILD-TYPE     3                         6   106
D3V7, multiclass
                           clus
vv                          ANKLE1 MUTATED ANKLE1 WILD-TYPE
  ASIAN                                  1                3
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  9              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                  cls
clus                0  1
  ANKLE1 MUTATED    1 10
  ANKLE1 WILD-TYPE 10 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKLE1 MUTATED      1   10
  ANKLE1 WILD-TYPE   10   99
                        clus
vv                       ANKLE1 MUTATED ANKLE1 WILD-TYPE
  HISPANIC OR LATINO                  1               10
  NOT HISPANIC OR LATINO             10               99
[1] 2 2
[1] FALSE

Clustering(4) Variable = FAM104B MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  FAM104B MUTATED     6   0
  FAM104B WILD-TYPE 120   4
  FAM104B MUTATED FAM104B WILD-TYPE 
                6               124 
  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 
       95.67         2.73         1.38         5.06        12.07        54.35 

$`FAM104B WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 
        6.08       122.50       212.65       161.72       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
        4.83        20.68        18.15         9.14        13.58        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         3.52        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-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        3.65         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
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         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  FAM104B MUTATED FAM104B WILD-TYPE 
             1.38              0.10 
  FAM104B MUTATED FAM104B WILD-TYPE 
            95.67            229.22 
  FAM104B MUTATED FAM104B WILD-TYPE 
            8.565            38.825 
[1] "1.4 - 95.7 (8.6)"   "0.1 - 229.2 (38.8)"
[1] "hr="     "2.6e+07"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM104B MUTATED         2        1        1        1         0         0
  FAM104B WILD-TYPE      17       23       10        4         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
                   vv
clus                STAGE IS
  FAM104B MUTATED          0
  FAM104B WILD-TYPE       46
D4V3, multiclass
            clus
vv           FAM104B MUTATED FAM104B WILD-TYPE
  STAGE I                  2                17
  STAGE IA                 1                23
  STAGE IB                 1                10
  STAGE II                 1                 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
  STAGE IS                 0                46
[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 69 48  6
D4V4, multiclass
    clus
vv   FAM104B MUTATED FAM104B WILD-TYPE
  T1               4                69
  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 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104B MUTATED      4    0
  FAM104B WILD-TYPE  108    4
   clus
vv  FAM104B MUTATED FAM104B WILD-TYPE
  0               4               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM104B MUTATED       0                         0     5
  FAM104B WILD-TYPE     4                         6   110
D4V7, multiclass
                           clus
vv                          FAM104B MUTATED FAM104B WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5               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"
D4V8, binary
                   cls
clus                  0   1
  FAM104B MUTATED     1   4
  FAM104B WILD-TYPE  10 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104B MUTATED      1    4
  FAM104B WILD-TYPE   10  105
                        clus
vv                       FAM104B MUTATED FAM104B WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               4               105
[1] 2 2
[1] FALSE

Clustering(5) Variable = DDX11 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  DDX11 MUTATED     6   0
  DDX11 WILD-TYPE 120   4
  DDX11 MUTATED DDX11 WILD-TYPE 
              6             124 
  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        72.85       161.72         9.14         3.65         5.29 

$`DDX11 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        40.70        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      212.65        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       20.68        18.15        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         3.52        37.18        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 TCGA-WZ-A7V4 
       35.61        33.07        23.90        41.52        24.26         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I 
       54.35        31.92        21.96         0.56        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  DDX11 MUTATED DDX11 WILD-TYPE 
           3.65            0.10 
  DDX11 MUTATED DDX11 WILD-TYPE 
         161.72          229.22 
  DDX11 MUTATED DDX11 WILD-TYPE 
         22.635          38.825 
[1] "3.6 - 161.7 (22.6)" "0.1 - 229.2 (38.8)"
[1] "hr="     "2.6e+07"
D5V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX11 MUTATED         1        0        0        1         1         0
  DDX11 WILD-TYPE      18       24       11        4         4         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  DDX11 MUTATED           0         0          0          0          1        2
  DDX11 WILD-TYPE         1         2          1          6          4       44
D5V3, multiclass
            clus
vv           DDX11 MUTATED DDX11 WILD-TYPE
  STAGE I                1              18
  STAGE IA               0              24
  STAGE IB               0              11
  STAGE II               1               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             1               4
  STAGE IS               2              44
[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 68 49  6
D5V4, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  T1             5              68
  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
D5V5, multiclass
[1] "Remove cluster labels:" "DDX11 MUTATED"         
clus
  DDX11 MUTATED DDX11 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" "DDX11 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAG0 
"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" 
D5V6, binary
                 cls
clus                0   1
  DDX11 MUTATED     4   0
  DDX11 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      4    0
  DDX11 WILD-TYPE  108    4
   clus
vv  DDX11 MUTATED DDX11 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX11 MUTATED       0                         1     5
  DDX11 WILD-TYPE     4                         5   110
D5V7, multiclass
                           clus
vv                          DDX11 MUTATED DDX11 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 5             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"
D5V8, binary
                 cls
clus                0   1
  DDX11 MUTATED     0   5
  DDX11 WILD-TYPE  11 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      0    5
  DDX11 WILD-TYPE   11  104
                        clus
vv                       DDX11 MUTATED DDX11 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             5             104
[1] 2 2
[1] FALSE

Clustering(6) Variable = NRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     6   0
  NRAS WILD-TYPE 120   4
  NRAS MUTATED NRAS WILD-TYPE 
             6            124 
  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         5.06         7.89        41.69         8.32        54.35 

$`NRAS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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         3.52 
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-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52        24.26         3.65         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       53.03        93.93        12.07        16.87         8.88        67.66 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
       50.96         0.43        12.92        20.12         6.90        57.90 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  NRAS MUTATED NRAS WILD-TYPE 
          1.38           0.10 
  NRAS MUTATED NRAS WILD-TYPE 
         54.35         229.22 
  NRAS MUTATED NRAS WILD-TYPE 
         8.105         38.825 
[1] "1.4 - 54.4 (8.1)"   "0.1 - 229.2 (38.8)"
[1] "hr="     "2.6e+07"
D6V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRAS MUTATED         1        3        1        0         0         0
  NRAS WILD-TYPE      18       21       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  NRAS MUTATED           0         0          0          0          0        0
  NRAS WILD-TYPE         1         2          1          6          5       46
D6V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               1             18
  STAGE IA              3             21
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              0             46
[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 68 49  6
D6V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            5             68
  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
D6V5, multiclass
D6V6, binary
                cls
clus               0   1
  NRAS MUTATED     4   0
  NRAS WILD-TYPE 108   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    0
  NRAS WILD-TYPE  108    4
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            4            108
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       1                         0     4
  NRAS WILD-TYPE     3                         6   111
D6V7, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D6V8, binary
                cls
clus               0   1
  NRAS MUTATED     0   5
  NRAS WILD-TYPE  11 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    5
  NRAS WILD-TYPE   11  104
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(7) Variable = PNPLA4 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PNPLA4 MUTATED     5   0
  PNPLA4 WILD-TYPE 121   4
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               5              125 
  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       108.16        98.53        12.07        54.35 

$`PNPLA4 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        40.70        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90       125.69        61.84        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF 
       93.93         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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       57.90        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
           12.07             0.10 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
          108.16           229.22 
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
           54.35            37.68 
[1] "12.1 - 108.2 (54.4)" "0.1 - 229.2 (37.7)" 
[1] "hr="     "2.6e+07"
D7V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNPLA4 MUTATED         0        1        2        0         1         0
  PNPLA4 WILD-TYPE      19       23        9        5         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
                  vv
clus               STAGE IS
  PNPLA4 MUTATED          1
  PNPLA4 WILD-TYPE       45
D7V3, multiclass
            clus
vv           PNPLA4 MUTATED PNPLA4 WILD-TYPE
  STAGE I                 0               19
  STAGE IA                1               23
  STAGE IB                2                9
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 72 46  6
D7V4, multiclass
    clus
vv   PNPLA4 MUTATED PNPLA4 WILD-TYPE
  T1              1               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
  PNPLA4 MUTATED    1     1
  PNPLA4 WILD-TYPE 44    11
D7V5, multiclass
[1] "Remove cluster labels:" "PNPLA4 MUTATED"        
clus
  PNPLA4 MUTATED PNPLA4 WILD-TYPE 
               2               55 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" "PNPLA4 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAG0 
"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" 
D7V6, binary
                  cls
clus                 0   1
  PNPLA4 MUTATED     4   0
  PNPLA4 WILD-TYPE 108   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA4 MUTATED      4    0
  PNPLA4 WILD-TYPE  108    4
   clus
vv  PNPLA4 MUTATED PNPLA4 WILD-TYPE
  0              4              108
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PNPLA4 MUTATED       0                         0     4
  PNPLA4 WILD-TYPE     4                         6   111
D7V7, multiclass
                           clus
vv                          PNPLA4 MUTATED PNPLA4 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D7V8, binary
                  cls
clus                 0   1
  PNPLA4 MUTATED     1   3
  PNPLA4 WILD-TYPE  10 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA4 MUTATED      1    3
  PNPLA4 WILD-TYPE   10  106
                        clus
vv                       PNPLA4 MUTATED PNPLA4 WILD-TYPE
  HISPANIC OR LATINO                  1               10
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(8) Variable = SERINC2 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  SERINC2 MUTATED     3   0
  SERINC2 WILD-TYPE 123   4
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                3               127 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
                0                 4 
$`SERINC2 MUTATED`
TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAHN 
       72.85        79.76        91.43 

$`SERINC2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.22        68.38        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        59.80       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  SERINC2 MUTATED SERINC2 WILD-TYPE 
            72.85              0.10 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
            91.43            229.22 
  SERINC2 MUTATED SERINC2 WILD-TYPE 
            79.76             37.18 
[1] "72.8 - 91.4 (79.8)" "0.1 - 229.2 (37.2)"
[1] "hr="     "2.5e+07"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERINC2 MUTATED         1        0        0        0         0         0
  SERINC2 WILD-TYPE      18       24       11        5         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
                   vv
clus                STAGE IS
  SERINC2 MUTATED          2
  SERINC2 WILD-TYPE       44
D8V3, multiclass
            clus
vv           SERINC2 MUTATED SERINC2 WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 0                24
  STAGE IB                 0                11
  STAGE II                 0                 5
  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
  STAGE IS                 2                44
[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 71 49  6
D8V4, multiclass
    clus
vv   SERINC2 MUTATED SERINC2 WILD-TYPE
  T1               2                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
  SERINC2 MUTATED    3     0
  SERINC2 WILD-TYPE 42    12
D8V5, multiclass
       clus
vv      SERINC2 MUTATED SERINC2 WILD-TYPE
  N0                  3                42
  N1+N2               0                12
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  SERINC2 MUTATED     3   0
  SERINC2 WILD-TYPE 109   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERINC2 MUTATED      3    0
  SERINC2 WILD-TYPE  109    4
   clus
vv  SERINC2 MUTATED SERINC2 WILD-TYPE
  0               3               109
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERINC2 MUTATED       0                         0     3
  SERINC2 WILD-TYPE     4                         6   112
D8V7, multiclass
                           clus
vv                          SERINC2 MUTATED SERINC2 WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3               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"
D8V8, binary
                   cls
clus                  0   1
  SERINC2 MUTATED     0   3
  SERINC2 WILD-TYPE  11 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERINC2 MUTATED      0    3
  SERINC2 WILD-TYPE   11  106
                        clus
vv                       SERINC2 MUTATED SERINC2 WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               3               106
[1] 2 2
[1] FALSE

Clustering(9) Variable = RBM10 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED     4   0
  RBM10 WILD-TYPE 122   4
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             126 
  RBM10 MUTATED RBM10 WILD-TYPE 
              0               4 
$`RBM10 MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAH0 TCGA-2G-AAL5 
       59.70       122.40        60.26       184.41 

$`RBM10 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAFG TCGA-2G-AAFH 
       20.32        30.35        38.30       102.35       191.31        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH2 
      128.94        61.45       170.33        80.94        60.16        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
      161.72        95.67       229.22       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  RBM10 MUTATED RBM10 WILD-TYPE 
           59.7             0.1 
  RBM10 MUTATED RBM10 WILD-TYPE 
         184.41          229.22 
  RBM10 MUTATED RBM10 WILD-TYPE 
          91.33           37.10 
[1] "59.7 - 184.4 (91.3)" "0.1 - 229.2 (37.1)" 
[1] "hr="     "2.6e+07"
D9V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM10 MUTATED         2        1        0        0         0         0
  RBM10 WILD-TYPE      17       23       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RBM10 MUTATED           0         0          0          0          0        1
  RBM10 WILD-TYPE         1         2          1          6          5       45
D9V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                2              17
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               1              45
[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 70 49  6
D9V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             3              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
  RBM10 MUTATED    3     0
  RBM10 WILD-TYPE 42    12
D9V5, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  N0                3              42
  N1+N2             0              12
[1] 2 2
[1] FALSE
D9V6, binary
                 cls
clus                0   1
  RBM10 MUTATED     4   0
  RBM10 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4    0
  RBM10 WILD-TYPE  108    4
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       0                         0     4
  RBM10 WILD-TYPE     4                         6   111
D9V7, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D9V8, binary
                 cls
clus                0   1
  RBM10 MUTATED     0   4
  RBM10 WILD-TYPE  11 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0    4
  RBM10 WILD-TYPE   11  105
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEK MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 121   4
  DEK MUTATED DEK WILD-TYPE 
            5           125 
  DEK MUTATED DEK WILD-TYPE 
            0             4 
$`DEK MUTATED`
TCGA-2G-AAFG TCGA-2G-AAGC TCGA-2G-AAHP TCGA-W4-A7U2 TCGA-XE-A8H5 
      191.31        72.85       176.15        41.52        40.01 

$`DEK WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        59.80        91.43         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U4 TCGA-WZ-A7V3 
       24.99        35.61        33.07        23.90        24.26         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  DEK MUTATED DEK WILD-TYPE 
        40.01          0.10 
  DEK MUTATED DEK WILD-TYPE 
       191.31        229.22 
  DEK MUTATED DEK WILD-TYPE 
        72.85         37.02 
[1] "40.0 - 191.3 (72.8)" "0.1 - 229.2 (37.0)" 
[1] "hr="     "2.6e+07"
D10V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DEK MUTATED         0        0        0        0         0         0
  DEK WILD-TYPE      19       24       11        5         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  DEK MUTATED           0         0          0          0          0        4
  DEK WILD-TYPE         1         2          1          6          5       42
D10V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0            19
  STAGE IA             0            24
  STAGE IB             0            11
  STAGE II             0             5
  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
  STAGE IS             4            42
[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 69 49  6
D10V4, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           4            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
  DEK MUTATED    3     0
  DEK WILD-TYPE 42    12
D10V5, multiclass
       clus
vv      DEK MUTATED DEK WILD-TYPE
  N0              3            42
  N1+N2           0            12
[1] 2 2
[1] FALSE
D10V6, binary
               cls
clus              0   1
  DEK MUTATED     4   0
  DEK WILD-TYPE 108   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    0
  DEK WILD-TYPE  108    4
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           4           108
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEK MUTATED       0                         0     4
  DEK WILD-TYPE     4                         6   111
D10V7, multiclass
                           clus
vv                          DEK MUTATED DEK WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               4           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"
D10V8, binary
               cls
clus              0   1
  DEK MUTATED     1   4
  DEK WILD-TYPE  10 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      1    4
  DEK WILD-TYPE   10  105
                        clus
vv                       DEK MUTATED DEK WILD-TYPE
  HISPANIC OR LATINO               1            10
  NOT HISPANIC OR LATINO           4           105
[1] 2 2
[1] FALSE

Clustering(11) Variable = ERC1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  ERC1 MUTATED     6   0
  ERC1 WILD-TYPE 120   4
  ERC1 MUTATED ERC1 WILD-TYPE 
             6            124 
  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 
       63.22       106.39        61.84         0.10         0.82        34.22 

$`ERC1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        71.24        72.20        61.71        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      108.16        59.64       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90       125.69        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW 
        2.73         0.13         3.52         7.00         4.83        20.68 
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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        5.06         0.16        28.14         6.87        18.38        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        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 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  ERC1 MUTATED ERC1 WILD-TYPE 
          0.10           0.13 
  ERC1 MUTATED ERC1 WILD-TYPE 
        106.39         229.22 
  ERC1 MUTATED ERC1 WILD-TYPE 
         48.03          37.99 
[1] "0.1 - 106.4 (48.0)" "0.1 - 229.2 (38.0)"
[1] "hr="     "2.6e+07"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERC1 MUTATED         0        1        1        0         0         0
  ERC1 WILD-TYPE      19       23       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  ERC1 MUTATED           0         0          0          1          1        1
  ERC1 WILD-TYPE         1         2          1          5          4       45
D11V3, multiclass
            clus
vv           ERC1 MUTATED ERC1 WILD-TYPE
  STAGE I               0             19
  STAGE IA              1             23
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              1             45
[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 71 47  5
D11V4, multiclass
    clus
vv   ERC1 MUTATED ERC1 WILD-TYPE
  T1            2             71
  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
D11V5, multiclass
       clus
vv      ERC1 MUTATED ERC1 WILD-TYPE
  N0               2             43
  N1+N2            1             11
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus               0   1
  ERC1 MUTATED     6   0
  ERC1 WILD-TYPE 106   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC1 MUTATED      6    0
  ERC1 WILD-TYPE  106    4
   clus
vv  ERC1 MUTATED ERC1 WILD-TYPE
  0            6            106
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERC1 MUTATED       0                         0     6
  ERC1 WILD-TYPE     4                         6   109
D11V7, multiclass
                           clus
vv                          ERC1 MUTATED ERC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                6            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                cls
clus               0   1
  ERC1 MUTATED     0   6
  ERC1 WILD-TYPE  11 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC1 MUTATED      0    6
  ERC1 WILD-TYPE   11  103
                        clus
vv                       ERC1 MUTATED ERC1 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            6            103
[1] 2 2
[1] FALSE

Clustering(12) Variable = HSF4 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  HSF4 MUTATED     6   0
  HSF4 WILD-TYPE 120   4
  HSF4 MUTATED HSF4 WILD-TYPE 
             6            124 
  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 
        9.57        60.26        98.53       212.65        67.66        31.92 

$`HSF4 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN 
      191.31        36.99        14.14        14.56        17.16        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90       125.69        61.84        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKH 
       59.80        91.43       176.15         6.08       122.50       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        93.93 
TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ 
       12.07         7.89        16.87         8.88        41.69        50.96 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P 
        0.43         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       54.35        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  HSF4 MUTATED HSF4 WILD-TYPE 
          9.57           0.10 
  HSF4 MUTATED HSF4 WILD-TYPE 
        212.65         229.22 
  HSF4 MUTATED HSF4 WILD-TYPE 
         63.96          37.43 
[1] "9.6 - 212.7 (64.0)" "0.1 - 229.2 (37.4)"
[1] "hr="     "2.6e+07"
D12V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSF4 MUTATED         1        1        2        0         1         0
  HSF4 WILD-TYPE      18       23        9        5         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  HSF4 MUTATED           0         0          0          0          0        1
  HSF4 WILD-TYPE         1         2          1          6          5       45
D12V3, multiclass
            clus
vv           HSF4 MUTATED HSF4 WILD-TYPE
  STAGE I               1             18
  STAGE IA              1             23
  STAGE IB              2              9
  STAGE II              0              5
  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
  STAGE IS              1             45
[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 71 46  6
D12V4, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  T1            2             71
  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-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1     TCGA-2G-AAF4 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG     TCGA-2G-AAFH 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL     TCGA-2G-AAFN 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY     TCGA-2G-AAG0 
"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 107   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      5    0
  HSF4 WILD-TYPE  107    4
   clus
vv  HSF4 MUTATED HSF4 WILD-TYPE
  0            5            107
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSF4 MUTATED       0                         0     6
  HSF4 WILD-TYPE     4                         6   109
D12V7, multiclass
                           clus
vv                          HSF4 MUTATED HSF4 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                6            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                cls
clus               0   1
  HSF4 MUTATED     0   5
  HSF4 WILD-TYPE  11 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      0    5
  HSF4 WILD-TYPE   11  104
                        clus
vv                       HSF4 MUTATED HSF4 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(13) Variable = MUC6 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  MUC6 MUTATED    13   0
  MUC6 WILD-TYPE 113   4
  MUC6 MUTATED MUC6 WILD-TYPE 
            13            117 
  MUC6 MUTATED MUC6 WILD-TYPE 
             0              4 
$`MUC6 MUTATED`
TCGA-2G-AAFJ TCGA-2G-AAFO TCGA-2G-AAG3 TCGA-2G-AAGN TCGA-2G-AAGW TCGA-2G-AAHC 
       14.56        16.50        52.37       106.39        61.45        59.74 
TCGA-2G-AAHN TCGA-2G-AAKG TCGA-S6-A8JW TCGA-W4-A7U4 TCGA-XE-A8H4 TCGA-XE-A8H5 
       91.43       212.65        20.68        24.26        18.38        40.01 
TCGA-XY-A9T9 
        6.90 

$`MUC6 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.14        17.16         9.57        14.86 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG5 TCGA-2G-AAG6 
       40.70        36.13        36.89        40.01        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       79.76        67.96        92.09        75.09       108.16        59.64 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX 
      115.00       120.62        59.28       124.57       128.94       170.33 
TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 
       80.94        60.16        60.26        59.84        59.90       125.69 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT 
       61.84        98.53        59.80        59.80       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        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         3.52        37.18        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 
       24.99        35.61        33.07        23.90        41.52         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-AANI 
        5.06         0.16         0.82        28.14         6.87        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        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-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
        8.32        12.92        20.12        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L 
       21.96         0.56         5.29        58.88         7.96        40.96 
TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E 
        8.15        37.02        39.35        27.55        17.39        16.41 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       11.34        46.88        10.85 

  MUC6 MUTATED MUC6 WILD-TYPE 
           6.9            0.1 
  MUC6 MUTATED MUC6 WILD-TYPE 
        212.65         229.22 
  MUC6 MUTATED MUC6 WILD-TYPE 
         40.01          37.68 
[1] "6.9 - 212.7 (40.0)" "0.1 - 229.2 (37.7)"
[1] "hr="     "7.9e+07"
D13V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC6 MUTATED         3        1        0        0         1         0
  MUC6 WILD-TYPE      16       23       11        5         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  MUC6 MUTATED           0         0          0          1          0        6
  MUC6 WILD-TYPE         1         2          1          5          5       40
D13V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  STAGE I               3             16
  STAGE IA              1             23
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              6             40
[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 64 47  6
D13V4, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  T1            9             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
  MUC6 MUTATED    4     2
  MUC6 WILD-TYPE 41    10
D13V5, multiclass
       clus
vv      MUC6 MUTATED MUC6 WILD-TYPE
  N0               4             41
  N1+N2            2             10
[1] 2 2
[1] FALSE
D13V6, binary
                cls
clus              0  1
  MUC6 MUTATED   13  0
  MUC6 WILD-TYPE 99  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     13    0
  MUC6 WILD-TYPE   99    4
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           13             99
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC6 MUTATED       1                         0    11
  MUC6 WILD-TYPE     3                         6   104
D13V7, multiclass
                           clus
vv                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               11            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"
D13V8, binary
                cls
clus              0  1
  MUC6 MUTATED    1 12
  MUC6 WILD-TYPE 10 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      1   12
  MUC6 WILD-TYPE   10   97
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                1             10
  NOT HISPANIC OR LATINO           12             97
[1] 2 2
[1] FALSE

Clustering(14) Variable = FANK1 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  FANK1 MUTATED     4   0
  FANK1 WILD-TYPE 122   4
  FANK1 MUTATED FANK1 WILD-TYPE 
              4             126 
  FANK1 MUTATED FANK1 WILD-TYPE 
              0               4 
$`FANK1 MUTATED`
TCGA-2G-AAFN TCGA-2G-AAKL TCGA-WZ-A8D5 TCGA-XE-A8H5 
       14.86        95.67         0.82        40.01 

$`FANK1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       212.65       161.72       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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-X3-A8G4 TCGA-XE-A8H1 
       24.26         3.65         5.06         0.16        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       18.38        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  FANK1 MUTATED FANK1 WILD-TYPE 
           0.82            0.10 
  FANK1 MUTATED FANK1 WILD-TYPE 
          95.67          229.22 
  FANK1 MUTATED FANK1 WILD-TYPE 
         27.435          37.990 
[1] "0.8 - 95.7 (27.4)"  "0.1 - 229.2 (38.0)"
[1] "hr="     "2.5e+07"
D14V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FANK1 MUTATED         0        0        0        1         0         0
  FANK1 WILD-TYPE      19       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  FANK1 MUTATED           0         0          0          1          0        1
  FANK1 WILD-TYPE         1         2          1          5          5       45
D14V3, multiclass
            clus
vv           FANK1 MUTATED FANK1 WILD-TYPE
  STAGE I                0              19
  STAGE IA               0              24
  STAGE IB               0              11
  STAGE II               1               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
  STAGE IS               1              45
[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 72 48  5
D14V4, multiclass
    clus
vv   FANK1 MUTATED FANK1 WILD-TYPE
  T1             1              72
  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
D14V5, multiclass
[1] "Remove cluster labels:" "FANK1 MUTATED"         
clus
  FANK1 MUTATED FANK1 WILD-TYPE 
              1              56 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" "FANK1 WILD-TYPE" 
     TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY      TCGA-2G-AAG0 
"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" 
D14V6, binary
                 cls
clus                0   1
  FANK1 MUTATED     4   0
  FANK1 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      4    0
  FANK1 WILD-TYPE  108    4
   clus
vv  FANK1 MUTATED FANK1 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FANK1 MUTATED       0                         0     3
  FANK1 WILD-TYPE     4                         6   112
D14V7, multiclass
                           clus
vv                          FANK1 MUTATED FANK1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D14V8, binary
                 cls
clus                0   1
  FANK1 MUTATED     1   3
  FANK1 WILD-TYPE  10 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANK1 MUTATED      1    3
  FANK1 WILD-TYPE   10  106
                        clus
vv                       FANK1 MUTATED FANK1 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(15) Variable = MLLT3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  MLLT3 MUTATED     3   0
  MLLT3 WILD-TYPE 123   4
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              3             127 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              0               4 
$`MLLT3 MUTATED`
TCGA-2G-AAHN TCGA-2G-AAKH TCGA-SN-A84Y 
       91.43       161.72        17.23 

$`MLLT3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT 
       98.53        59.74        59.80        59.80       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       212.65        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84X TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
       16.31         9.63        10.26         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  MLLT3 MUTATED MLLT3 WILD-TYPE 
          17.23            0.10 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
         161.72          229.22 
  MLLT3 MUTATED MLLT3 WILD-TYPE 
          91.43           37.68 
[1] "17.2 - 161.7 (91.4)" "0.1 - 229.2 (37.7)" 
[1] "hr="     "2.5e+07"
D15V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLLT3 MUTATED         1        0        0        1         0         0
  MLLT3 WILD-TYPE      18       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  MLLT3 MUTATED           0         0          0          0          0        1
  MLLT3 WILD-TYPE         1         2          1          6          5       45
D15V3, multiclass
            clus
vv           MLLT3 MUTATED MLLT3 WILD-TYPE
  STAGE I                1              18
  STAGE IA               0              24
  STAGE IB               0              11
  STAGE II               1               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
  STAGE IS               1              45
[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 71 49  6
D15V4, multiclass
    clus
vv   MLLT3 MUTATED MLLT3 WILD-TYPE
  T1             2              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
  MLLT3 MUTATED    1     0
  MLLT3 WILD-TYPE 44    12
D15V5, multiclass
[1] "Remove cluster labels:" "MLLT3 MUTATED"         
clus
  MLLT3 MUTATED MLLT3 WILD-TYPE 
              1              56 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" "MLLT3 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D15V6, binary
                 cls
clus                0   1
  MLLT3 MUTATED     3   0
  MLLT3 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT3 MUTATED      3    0
  MLLT3 WILD-TYPE  109    4
   clus
vv  MLLT3 MUTATED MLLT3 WILD-TYPE
  0             3             109
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLLT3 MUTATED       0                         0     3
  MLLT3 WILD-TYPE     4                         6   112
D15V7, multiclass
                           clus
vv                          MLLT3 MUTATED MLLT3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D15V8, binary
                 cls
clus                0   1
  MLLT3 MUTATED     1   2
  MLLT3 WILD-TYPE  10 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT3 MUTATED      1    2
  MLLT3 WILD-TYPE   10  107
                        clus
vv                       MLLT3 MUTATED MLLT3 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(16) Variable = RHPN2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  RHPN2 MUTATED     5   1
  RHPN2 WILD-TYPE 121   3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6             124 
  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        36.89        71.24        59.80        95.67        21.96 

$`RHPN2 WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       30.35        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG6 
       16.50        40.70        36.13        40.01        52.37        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       79.76        67.96        92.09        75.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 
      229.22       184.41       131.21        70.59         2.73         0.13 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        3.52         7.00         0.10         4.83        20.68        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         3.52        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         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       54.35        31.92         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  RHPN2 MUTATED RHPN2 WILD-TYPE 
          20.32            0.10 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
          95.67          229.22 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         48.345          37.990 
[1] "20.3 - 95.7 (48.3)" "0.1 - 229.2 (38.0)"
[1] "hr=" "7.7"
D16V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHPN2 MUTATED         1        1        0        1         0         0
  RHPN2 WILD-TYPE      18       23       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RHPN2 MUTATED           0         1          0          0          0        2
  RHPN2 WILD-TYPE         1         1          1          6          5       44
D16V3, multiclass
            clus
vv           RHPN2 MUTATED RHPN2 WILD-TYPE
  STAGE I                1              18
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               1               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
  STAGE IS               2              44
[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 69 49  5
D16V4, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  T1             4              69
  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
D16V5, multiclass
       clus
vv      RHPN2 MUTATED RHPN2 WILD-TYPE
  N0                3              42
  N1+N2             0              12
[1] 2 2
[1] FALSE
D16V6, binary
                 cls
clus                0   1
  RHPN2 MUTATED     4   1
  RHPN2 WILD-TYPE 108   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      4    1
  RHPN2 WILD-TYPE  108    3
   clus
vv  RHPN2 MUTATED RHPN2 WILD-TYPE
  0             4             108
  1             1               3
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHPN2 MUTATED       0                         0     6
  RHPN2 WILD-TYPE     4                         6   109
D16V7, multiclass
                           clus
vv                          RHPN2 MUTATED RHPN2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 6             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                 cls
clus                0   1
  RHPN2 MUTATED     0   5
  RHPN2 WILD-TYPE  11 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      0    5
  RHPN2 WILD-TYPE   11  104
                        clus
vv                       RHPN2 MUTATED RHPN2 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             5             104
[1] 2 2
[1] FALSE

Clustering(17) Variable = SP8 MUTATION ANALYSIS
D17V1, survival
               sevent
clus2             0   1
  SP8 MUTATED     4   0
  SP8 WILD-TYPE 122   4
  SP8 MUTATED SP8 WILD-TYPE 
            4           126 
  SP8 MUTATED SP8 WILD-TYPE 
            0             4 
$`SP8 MUTATED`
TCGA-2G-AAFI TCGA-2G-AAGA TCGA-SN-A84X TCGA-XE-AANI 
       14.14        68.22        10.26        34.22 

$`SP8 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC 
       71.24        72.20        61.71        63.22        63.32        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84W TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
       16.31         9.63        17.23         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       18.38        40.01        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  SP8 MUTATED SP8 WILD-TYPE 
        10.26          0.10 
  SP8 MUTATED SP8 WILD-TYPE 
        68.22        229.22 
  SP8 MUTATED SP8 WILD-TYPE 
       24.180        38.825 
[1] "10.3 - 68.2 (24.2)" "0.1 - 229.2 (38.8)"
[1] "hr="     "2.5e+07"
D17V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP8 MUTATED         0        0        1        0         1         0
  SP8 WILD-TYPE      19       24       10        5         4         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  SP8 MUTATED           0         0          0          0          0        2
  SP8 WILD-TYPE         1         2          1          6          5       44
D17V3, multiclass
            clus
vv           SP8 MUTATED SP8 WILD-TYPE
  STAGE I              0            19
  STAGE IA             0            24
  STAGE IB             1            10
  STAGE II             0             5
  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
  STAGE IS             2            44
[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 71 48  6
D17V4, multiclass
    clus
vv   SP8 MUTATED SP8 WILD-TYPE
  T1           2            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
  SP8 MUTATED    1     1
  SP8 WILD-TYPE 44    11
D17V5, multiclass
[1] "Remove cluster labels:" "SP8 MUTATED"           
clus
  SP8 MUTATED SP8 WILD-TYPE 
            2            55 
   TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4    TCGA-2G-AAF6 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFJ    TCGA-2G-AAFL 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV    TCGA-2G-AAFY 
"SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" "SP8 WILD-TYPE" 
   TCGA-2G-AAG0    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" 
D17V6, binary
               cls
clus              0   1
  SP8 MUTATED     4   0
  SP8 WILD-TYPE 108   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP8 MUTATED      4    0
  SP8 WILD-TYPE  108    4
   clus
vv  SP8 MUTATED SP8 WILD-TYPE
  0           4           108
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP8 MUTATED       0                         0     4
  SP8 WILD-TYPE     4                         6   111
D17V7, multiclass
                           clus
vv                          SP8 MUTATED SP8 WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               4           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"
D17V8, binary
               cls
clus              0   1
  SP8 MUTATED     1   3
  SP8 WILD-TYPE  10 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP8 MUTATED      1    3
  SP8 WILD-TYPE   10  106
                        clus
vv                       SP8 MUTATED SP8 WILD-TYPE
  HISPANIC OR LATINO               1            10
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(18) Variable = KRTAP1-1 MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  KRTAP1-1 MUTATED     3   0
  KRTAP1-1 WILD-TYPE 123   4
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                127 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 0                  4 
$`KRTAP1-1 MUTATED`
TCGA-2G-AAFI TCGA-WZ-A8D5 TCGA-XE-AAOF 
       14.14         0.82        41.69 

$`KRTAP1-1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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         3.65         5.06         0.16        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        50.96         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
              0.82               0.10 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             41.69             229.22 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             14.14              38.30 
[1] "0.8 - 41.7 (14.1)"  "0.1 - 229.2 (38.3)"
[1] "hr="     "9100000"
D18V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP1-1 MUTATED         0        1        1        0         0         0
  KRTAP1-1 WILD-TYPE      19       23       10        5         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
                    vv
clus                 STAGE IS
  KRTAP1-1 MUTATED          0
  KRTAP1-1 WILD-TYPE       46
D18V3, multiclass
[1] "Remove cluster labels:" "KRTAP1-1 MUTATED"      
clus
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 2                124 
        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-AAFJ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFL         TCGA-2G-AAFM         TCGA-2G-AAFN 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFO         TCGA-2G-AAFV         TCGA-2G-AAFY 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFZ         TCGA-2G-AAG0         TCGA-2G-AAG3 
"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-AAGV         TCGA-2G-AAGW 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAGX         TCGA-2G-AAGY         TCGA-2G-AAGZ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAH0         TCGA-2G-AAH2         TCGA-2G-AAH3 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAH4         TCGA-2G-AAH8         TCGA-2G-AAHA 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHC         TCGA-2G-AAHG         TCGA-2G-AAHL 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAHN         TCGA-2G-AAHP         TCGA-2G-AAHT 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAKD         TCGA-2G-AAKG         TCGA-2G-AAKH 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAKL         TCGA-2G-AAKM         TCGA-2G-AAL5 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAL7         TCGA-2G-AALP         TCGA-2X-A9D5 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2X-A9D6         TCGA-4K-AA1G         TCGA-4K-AA1H 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-4K-AA1I         TCGA-4K-AAAL         TCGA-S6-A8JW 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-S6-A8JX         TCGA-S6-A8JY         TCGA-SB-A6J6 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-SN-A6IS         TCGA-SN-A84W         TCGA-SN-A84X 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-SN-A84Y         TCGA-SO-A8JP         TCGA-VF-A8A8 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VF-A8AA         TCGA-VF-A8AB         TCGA-VF-A8AC 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-VF-A8AD         TCGA-VF-A8AE         TCGA-WZ-A7V3 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-WZ-A7V4         TCGA-WZ-A7V5         TCGA-X3-A8G4 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-XE-A8H1         TCGA-XE-A8H4         TCGA-XE-A8H5 
"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-AA0E         TCGA-ZM-AA0F         TCGA-ZM-AA0H 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-ZM-AA0N 
"KRTAP1-1 WILD-TYPE" 
                    vv
clus                 T1 T2 T3
  KRTAP1-1 MUTATED    1  1  1
  KRTAP1-1 WILD-TYPE 72 49  5
D18V4, multiclass
    clus
vv   KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  T1                1                 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
  KRTAP1-1 MUTATED    1     0
  KRTAP1-1 WILD-TYPE 44    12
D18V5, multiclass
[1] "Remove cluster labels:" "KRTAP1-1 MUTATED"      
clus
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 1                 56 
        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-AAFJ 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFL         TCGA-2G-AAFM         TCGA-2G-AAFN 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAFO         TCGA-2G-AAFV         TCGA-2G-AAFY 
"KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" "KRTAP1-1 WILD-TYPE" 
        TCGA-2G-AAG0         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" 
D18V6, binary
                    cls
clus                   0   1
  KRTAP1-1 MUTATED     3   0
  KRTAP1-1 WILD-TYPE 109   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      3    0
  KRTAP1-1 WILD-TYPE  109    4
   clus
vv  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  0                3                109
  1                0                  4
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP1-1 MUTATED       1                         0     2
  KRTAP1-1 WILD-TYPE     3                         6   113
D18V7, multiclass
                           clus
vv                          KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  ASIAN                                    1                  3
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    2                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"
D18V8, binary
                    cls
clus                   0   1
  KRTAP1-1 MUTATED     0   3
  KRTAP1-1 WILD-TYPE  11 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      0    3
  KRTAP1-1 WILD-TYPE   11  106
                        clus
vv                       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                3                106
[1] 2 2
[1] FALSE

Clustering(19) Variable = ANKRD11 MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2                 0   1
  ANKRD11 MUTATED     5   0
  ANKRD11 WILD-TYPE 121   4
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                5               125 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                0                 4 
$`ANKRD11 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAHA TCGA-VF-A8AB TCGA-XE-AAO3 TCGA-YU-A90S 
       30.35        98.53        24.99        93.93        31.92 

$`ANKRD11 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHC 
       60.26        59.84        59.90       125.69        61.84        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        37.18 
TCGA-VF-A8AA TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-W4-A7U4 
       37.68        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
            24.99              0.10 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
            98.53            229.22 
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
            31.92             38.30 
[1] "25.0 - 98.5 (31.9)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.6e+07"
D19V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD11 MUTATED         1        2        1        0         0         0
  ANKRD11 WILD-TYPE      18       22       10        5         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
                   vv
clus                STAGE IS
  ANKRD11 MUTATED          1
  ANKRD11 WILD-TYPE       45
D19V3, multiclass
            clus
vv           ANKRD11 MUTATED ANKRD11 WILD-TYPE
  STAGE I                  1                18
  STAGE IA                 2                22
  STAGE IB                 1                10
  STAGE II                 0                 5
  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
  STAGE IS                 1                45
[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 70 48  6
D19V4, multiclass
    clus
vv   ANKRD11 MUTATED ANKRD11 WILD-TYPE
  T1               3                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
  ANKRD11 MUTATED    2     0
  ANKRD11 WILD-TYPE 43    12
D19V5, multiclass
[1] "Remove cluster labels:" "ANKRD11 MUTATED"       
clus
  ANKRD11 MUTATED ANKRD11 WILD-TYPE 
                2                55 
       TCGA-2G-AAEW        TCGA-2G-AAF1        TCGA-2G-AAF4        TCGA-2G-AAF6 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAF8        TCGA-2G-AAFG        TCGA-2G-AAFH        TCGA-2G-AAFI 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAFJ        TCGA-2G-AAFL        TCGA-2G-AAFM        TCGA-2G-AAFN 
"ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" "ANKRD11 WILD-TYPE" 
       TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY        TCGA-2G-AAG0 
"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" 
D19V6, binary
                   cls
clus                  0   1
  ANKRD11 MUTATED     4   0
  ANKRD11 WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD11 MUTATED      4    0
  ANKRD11 WILD-TYPE  108    4
   clus
vv  ANKRD11 MUTATED ANKRD11 WILD-TYPE
  0               4               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD11 MUTATED       1                         1     3
  ANKRD11 WILD-TYPE     3                         5   112
D19V7, multiclass
                           clus
vv                          ANKRD11 MUTATED ANKRD11 WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   3               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"
D19V8, binary
                   cls
clus                  0   1
  ANKRD11 MUTATED     0   4
  ANKRD11 WILD-TYPE  11 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD11 MUTATED      0    4
  ANKRD11 WILD-TYPE   11  105
                        clus
vv                       ANKRD11 MUTATED ANKRD11 WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               4               105
[1] 2 2
[1] FALSE

Clustering(20) Variable = SPIN2A MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  SPIN2A MUTATED     3   0
  SPIN2A WILD-TYPE 123   4
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               3              127 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               0                4 
$`SPIN2A MUTATED`
TCGA-2G-AAGK TCGA-SN-A6IS TCGA-SN-A84W 
      108.16        16.31         9.63 

$`SPIN2A WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       75.09        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        1.38        10.26        17.23         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  SPIN2A MUTATED SPIN2A WILD-TYPE 
            9.63             0.10 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
          108.16           229.22 
  SPIN2A MUTATED SPIN2A WILD-TYPE 
           16.31            38.30 
[1] "9.6 - 108.2 (16.3)" "0.1 - 229.2 (38.3)"
[1] "hr="     "9100000"
D20V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPIN2A MUTATED         0        0        0        0         0         0
  SPIN2A WILD-TYPE      19       24       11        5         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
                  vv
clus               STAGE IS
  SPIN2A MUTATED          3
  SPIN2A WILD-TYPE       43
D20V3, multiclass
            clus
vv           SPIN2A MUTATED SPIN2A WILD-TYPE
  STAGE I                 0               19
  STAGE IA                0               24
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                3               43
[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 72 48  6
D20V4, multiclass
    clus
vv   SPIN2A MUTATED SPIN2A WILD-TYPE
  T1              1               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
  SPIN2A MUTATED    1     0
  SPIN2A WILD-TYPE 44    12
D20V5, multiclass
[1] "Remove cluster labels:" "SPIN2A MUTATED"        
clus
  SPIN2A MUTATED SPIN2A WILD-TYPE 
               1               56 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" "SPIN2A WILD-TYPE" 
      TCGA-2G-AAG0       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" 
D20V6, binary
                  cls
clus                 0   1
  SPIN2A MUTATED     3   0
  SPIN2A WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIN2A MUTATED      3    0
  SPIN2A WILD-TYPE  109    4
   clus
vv  SPIN2A MUTATED SPIN2A WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPIN2A MUTATED       0                         0     3
  SPIN2A WILD-TYPE     4                         6   112
D20V7, multiclass
                           clus
vv                          SPIN2A MUTATED SPIN2A WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D20V8, binary
                  cls
clus                 0   1
  SPIN2A MUTATED     2   1
  SPIN2A WILD-TYPE   9 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPIN2A MUTATED      2    1
  SPIN2A WILD-TYPE    9  108
                        clus
vv                       SPIN2A MUTATED SPIN2A WILD-TYPE
  HISPANIC OR LATINO                  2                9
  NOT HISPANIC OR LATINO              1              108
[1] 2 2
[1] FALSE

Clustering(21) Variable = ATXN3 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ATXN3 MUTATED     3   0
  ATXN3 WILD-TYPE 123   4
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              3             127 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              0               4 
$`ATXN3 MUTATED`
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-XE-AAOC 
       61.45        60.16         8.88 

$`ATXN3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 
       59.28       124.57       128.94       170.33        80.94        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOD 
       53.03        93.93        12.07         7.89        16.87        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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  ATXN3 MUTATED ATXN3 WILD-TYPE 
           8.88            0.10 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
          61.45          229.22 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
          60.16           37.68 
[1] "8.9 - 61.5 (60.2)"  "0.1 - 229.2 (37.7)"
[1] "hr="     "9200000"
D21V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATXN3 MUTATED         0        1        0        0         0         0
  ATXN3 WILD-TYPE      19       23       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  ATXN3 MUTATED           0         0          1          0          0        1
  ATXN3 WILD-TYPE         1         2          0          6          5       45
D21V3, multiclass
            clus
vv           ATXN3 MUTATED ATXN3 WILD-TYPE
  STAGE I                0              19
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               1              45
[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 71 49  6
D21V4, multiclass
    clus
vv   ATXN3 MUTATED ATXN3 WILD-TYPE
  T1             2              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
  ATXN3 MUTATED    1     1
  ATXN3 WILD-TYPE 44    11
D21V5, multiclass
[1] "Remove cluster labels:" "ATXN3 MUTATED"         
clus
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" "ATXN3 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D21V6, binary
                 cls
clus                0   1
  ATXN3 MUTATED     2   1
  ATXN3 WILD-TYPE 110   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      2    1
  ATXN3 WILD-TYPE  110    3
   clus
vv  ATXN3 MUTATED ATXN3 WILD-TYPE
  0             2             110
  1             1               3
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATXN3 MUTATED       0                         0     3
  ATXN3 WILD-TYPE     4                         6   112
D21V7, multiclass
                           clus
vv                          ATXN3 MUTATED ATXN3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D21V8, binary
                 cls
clus                0   1
  ATXN3 MUTATED     1   2
  ATXN3 WILD-TYPE  10 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      1    2
  ATXN3 WILD-TYPE   10  107
                        clus
vv                       ATXN3 MUTATED ATXN3 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(22) Variable = SSBP3 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  SSBP3 MUTATED     3   0
  SSBP3 WILD-TYPE 123   4
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             127 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              0               4 
$`SSBP3 MUTATED`
TCGA-2G-AAFM TCGA-2G-AAFV TCGA-YU-A90P 
        9.57        40.70        57.90 

$`SSBP3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN 
      191.31        36.99        14.14        14.56        17.16        14.86 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       16.50        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
       20.12         6.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  SSBP3 MUTATED SSBP3 WILD-TYPE 
           9.57            0.10 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          57.90          229.22 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          40.70           37.68 
[1] "9.6 - 57.9 (40.7)"  "0.1 - 229.2 (37.7)"
[1] "hr="     "9200000"
D22V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SSBP3 MUTATED         0        1        0        0         1         0
  SSBP3 WILD-TYPE      19       23       11        5         4         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  SSBP3 MUTATED           0         0          0          0          0        1
  SSBP3 WILD-TYPE         1         2          1          6          5       45
D22V3, multiclass
            clus
vv           SSBP3 MUTATED SSBP3 WILD-TYPE
  STAGE I                0              19
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               1              45
[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 71 49  6
D22V4, multiclass
    clus
vv   SSBP3 MUTATED SSBP3 WILD-TYPE
  T1             2              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
  SSBP3 MUTATED    1     1
  SSBP3 WILD-TYPE 44    11
D22V5, multiclass
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFN 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2G-AAFO      TCGA-2G-AAFY      TCGA-2G-AAG0      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" 
D22V6, binary
                 cls
clus                0   1
  SSBP3 MUTATED     2   0
  SSBP3 WILD-TYPE 110   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    0
  SSBP3 WILD-TYPE  110    4
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             2             110
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSBP3 MUTATED       0                         0     3
  SSBP3 WILD-TYPE     4                         6   112
D22V7, multiclass
                           clus
vv                          SSBP3 MUTATED SSBP3 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D22V8, binary
                 cls
clus                0   1
  SSBP3 MUTATED     0   2
  SSBP3 WILD-TYPE  11 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      0    2
  SSBP3 WILD-TYPE   11  107
                        clus
vv                       SSBP3 MUTATED SSBP3 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(23) Variable = KRTAP10-10 MUTATION ANALYSIS
D23V1, survival
                      sevent
clus2                    0   1
  KRTAP10-10 MUTATED     4   0
  KRTAP10-10 WILD-TYPE 122   4
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   4                  126 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   0                    4 
$`KRTAP10-10 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAH2 TCGA-XE-AAOJ TCGA-ZM-AA0E 
       30.35        59.84        50.96        16.41 

$`KRTAP10-10 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.26        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        93.93        12.07         7.89        16.87         8.88 
TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 
       67.66        41.69         0.43         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       39.35        27.55        17.39        11.34        46.88        10.85 

  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
               16.41                 0.10 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
               59.84               229.22 
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
              40.655               37.990 
[1] "16.4 - 59.8 (40.7)" "0.1 - 229.2 (38.0)"
[1] "hr="     "2.6e+07"
D23V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP10-10 MUTATED         0        1        0        0         0         0
  KRTAP10-10 WILD-TYPE      19       23       11        5         5         1
                      vv
clus                   STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRTAP10-10 MUTATED           0         0          0          0          0
  KRTAP10-10 WILD-TYPE         1         2          1          6          5
                      vv
clus                   STAGE IS
  KRTAP10-10 MUTATED          3
  KRTAP10-10 WILD-TYPE       43
D23V3, multiclass
            clus
vv           KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  STAGE I                     0                   19
  STAGE IA                    1                   23
  STAGE IB                    0                   11
  STAGE II                    0                    5
  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
  STAGE IS                    3                   43
[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 69 50  6
D23V4, multiclass
    clus
vv   KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  T1                  4                   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
  KRTAP10-10 MUTATED    2     0
  KRTAP10-10 WILD-TYPE 43    12
D23V5, multiclass
[1] "Remove cluster labels:" "KRTAP10-10 MUTATED"    
clus
  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE 
                   2                   55 
          TCGA-2G-AAEW           TCGA-2G-AAF1           TCGA-2G-AAF4 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAF6           TCGA-2G-AAF8           TCGA-2G-AAFG 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFH           TCGA-2G-AAFI           TCGA-2G-AAFJ 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFL           TCGA-2G-AAFM           TCGA-2G-AAFN 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAFO           TCGA-2G-AAFV           TCGA-2G-AAFY 
"KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" "KRTAP10-10 WILD-TYPE" 
          TCGA-2G-AAG0           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" 
D23V6, binary
                      cls
clus                     0   1
  KRTAP10-10 MUTATED     4   0
  KRTAP10-10 WILD-TYPE 108   4
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-10 MUTATED      4    0
  KRTAP10-10 WILD-TYPE  108    4
   clus
vv  KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  0                  4                  108
  1                  0                    4
[1] 2 2
[1] FALSE
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-10 MUTATED       0                         0     4
  KRTAP10-10 WILD-TYPE     4                         6   111
D23V7, multiclass
                           clus
vv                          KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  ASIAN                                      0                    4
  BLACK OR AFRICAN AMERICAN                  0                    6
  WHITE                                      4                  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"
D23V8, binary
                      cls
clus                     0   1
  KRTAP10-10 MUTATED     1   3
  KRTAP10-10 WILD-TYPE  10 106
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-10 MUTATED      1    3
  KRTAP10-10 WILD-TYPE   10  106
                        clus
vv                       KRTAP10-10 MUTATED KRTAP10-10 WILD-TYPE
  HISPANIC OR LATINO                      1                   10
  NOT HISPANIC OR LATINO                  3                  106
[1] 2 2
[1] FALSE

Clustering(24) Variable = BCL11B MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  BCL11B MUTATED     5   0
  BCL11B WILD-TYPE 121   4
  BCL11B MUTATED BCL11B WILD-TYPE 
               5              125 
  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        21.96        39.35 

$`BCL11B WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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         3.65         5.06         0.16         0.82 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ 
       28.14         6.87        18.38        40.01        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 
        8.88        67.66        50.96         0.43         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90Y TCGA-YU-A912 
       20.12         6.90        57.90        54.35         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0B 
       58.88         7.96        40.96         8.15        37.02        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  BCL11B MUTATED BCL11B WILD-TYPE 
           21.96             0.10 
  BCL11B MUTATED BCL11B WILD-TYPE 
           52.37           229.22 
  BCL11B MUTATED BCL11B WILD-TYPE 
           39.35            37.68 
[1] "22.0 - 52.4 (39.4)" "0.1 - 229.2 (37.7)"
[1] "hr="     "2.6e+07"
D24V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL11B MUTATED         0        3        1        0         0         0
  BCL11B WILD-TYPE      19       21       10        5         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
                  vv
clus               STAGE IS
  BCL11B MUTATED          1
  BCL11B WILD-TYPE       45
D24V3, multiclass
            clus
vv           BCL11B MUTATED BCL11B WILD-TYPE
  STAGE I                 0               19
  STAGE IA                3               21
  STAGE IB                1               10
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 70 48  6
D24V4, multiclass
    clus
vv   BCL11B MUTATED BCL11B WILD-TYPE
  T1              3               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
  BCL11B MUTATED    0     0
  BCL11B WILD-TYPE 45    12
D24V5, multiclass
D24V6, binary
                  cls
clus                 0   1
  BCL11B MUTATED     3   0
  BCL11B WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11B MUTATED      3    0
  BCL11B WILD-TYPE  109    4
   clus
vv  BCL11B MUTATED BCL11B WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL11B MUTATED       1                         0     4
  BCL11B WILD-TYPE     3                         6   111
D24V7, multiclass
                           clus
vv                          BCL11B MUTATED BCL11B WILD-TYPE
  ASIAN                                  1                3
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D24V8, binary
                  cls
clus                 0   1
  BCL11B MUTATED     0   3
  BCL11B WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11B MUTATED      0    3
  BCL11B WILD-TYPE   11  106
                        clus
vv                       BCL11B MUTATED BCL11B WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(25) Variable = FAM101B MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  FAM101B MUTATED     4   0
  FAM101B WILD-TYPE 122   4
  FAM101B MUTATED FAM101B WILD-TYPE 
                4               126 
  FAM101B MUTATED FAM101B WILD-TYPE 
                0                 4 
$`FAM101B MUTATED`
TCGA-2G-AAFJ TCGA-SN-A84Y TCGA-VF-A8AE TCGA-XE-AAOL 
       14.56        17.23        23.90         0.43 

$`FAM101B WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.14        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52        37.18 
TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-W4-A7U2 TCGA-W4-A7U4 
       37.68        24.99        35.61        33.07        41.52        24.26 
TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  FAM101B MUTATED FAM101B WILD-TYPE 
             0.43              0.10 
  FAM101B MUTATED FAM101B WILD-TYPE 
            23.90            229.22 
  FAM101B MUTATED FAM101B WILD-TYPE 
           15.895            39.680 
[1] "0.4 - 23.9 (15.9)"  "0.1 - 229.2 (39.7)"
[1] "hr="     "9200000"
D25V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM101B MUTATED         2        1        0        0         0         0
  FAM101B WILD-TYPE      17       23       11        5         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
                   vv
clus                STAGE IS
  FAM101B MUTATED          1
  FAM101B WILD-TYPE       45
D25V3, multiclass
            clus
vv           FAM101B MUTATED FAM101B WILD-TYPE
  STAGE I                  2                17
  STAGE IA                 1                23
  STAGE IB                 0                11
  STAGE II                 0                 5
  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
  STAGE IS                 1                45
[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 70 49  6
D25V4, multiclass
    clus
vv   FAM101B MUTATED FAM101B WILD-TYPE
  T1               3                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
  FAM101B MUTATED    1     0
  FAM101B WILD-TYPE 44    12
D25V5, multiclass
[1] "Remove cluster labels:" "FAM101B MUTATED"       
clus
  FAM101B MUTATED FAM101B WILD-TYPE 
                1                56 
       TCGA-2G-AAEW        TCGA-2G-AAEX        TCGA-2G-AAF1        TCGA-2G-AAF4 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAF6        TCGA-2G-AAF8        TCGA-2G-AAFG        TCGA-2G-AAFH 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAFI        TCGA-2G-AAFL        TCGA-2G-AAFM        TCGA-2G-AAFN 
"FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" "FAM101B WILD-TYPE" 
       TCGA-2G-AAFO        TCGA-2G-AAFV        TCGA-2G-AAFY        TCGA-2G-AAG0 
"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" 
D25V6, binary
                   cls
clus                  0   1
  FAM101B MUTATED     4   0
  FAM101B WILD-TYPE 108   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM101B MUTATED      4    0
  FAM101B WILD-TYPE  108    4
   clus
vv  FAM101B MUTATED FAM101B WILD-TYPE
  0               4               108
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM101B MUTATED       1                         1     2
  FAM101B WILD-TYPE     3                         5   113
D25V7, multiclass
                           clus
vv                          FAM101B MUTATED FAM101B WILD-TYPE
  ASIAN                                   1                 3
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   2               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"
D25V8, binary
                   cls
clus                  0   1
  FAM101B MUTATED     1   3
  FAM101B WILD-TYPE  10 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM101B MUTATED      1    3
  FAM101B WILD-TYPE   10  106
                        clus
vv                       FAM101B MUTATED FAM101B WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               3               106
[1] 2 2
[1] FALSE

Clustering(26) Variable = PSMD11 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  PSMD11 MUTATED     4   0
  PSMD11 WILD-TYPE 122   4
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               4              126 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               0                4 
$`PSMD11 MUTATED`
TCGA-2G-AAEX TCGA-WZ-A7V5 TCGA-XE-AAO6 TCGA-XY-A89B 
       30.35         0.16         7.89         8.32 

$`PSMD11 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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-A8D5 TCGA-X3-A8G4 
       41.52        24.26         3.65         5.06         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD 
       53.03        93.93        12.07        16.87         8.88        67.66 
TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       41.69        50.96         0.43        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  PSMD11 MUTATED PSMD11 WILD-TYPE 
            0.16             0.10 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           30.35           229.22 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           8.105           39.680 
[1] "0.2 - 30.4 (8.1)"   "0.1 - 229.2 (39.7)"
[1] "hr="     "9100000"
D26V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSMD11 MUTATED         1        2        0        0         0         0
  PSMD11 WILD-TYPE      18       22       11        5         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
                  vv
clus               STAGE IS
  PSMD11 MUTATED          1
  PSMD11 WILD-TYPE       45
D26V3, multiclass
            clus
vv           PSMD11 MUTATED PSMD11 WILD-TYPE
  STAGE I                 1               18
  STAGE IA                2               22
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 70 49  6
D26V4, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  T1              3               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
  PSMD11 MUTATED    1     0
  PSMD11 WILD-TYPE 44    12
D26V5, multiclass
[1] "Remove cluster labels:" "PSMD11 MUTATED"        
clus
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               1               56 
      TCGA-2G-AAEW       TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN 
"PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" "PSMD11 WILD-TYPE" 
      TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAG0 
"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" 
D26V6, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     3   0
  PSMD11 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      3    0
  PSMD11 WILD-TYPE  109    4
   clus
vv  PSMD11 MUTATED PSMD11 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSMD11 MUTATED       0                         0     4
  PSMD11 WILD-TYPE     4                         6   111
D26V7, multiclass
                           clus
vv                          PSMD11 MUTATED PSMD11 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              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"
D26V8, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     0   4
  PSMD11 WILD-TYPE  11 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      0    4
  PSMD11 WILD-TYPE   11  105
                        clus
vv                       PSMD11 MUTATED PSMD11 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              4              105
[1] 2 2
[1] FALSE

Clustering(27) Variable = FAM8A1 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  FAM8A1 MUTATED     3   0
  FAM8A1 WILD-TYPE 123   4
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               3              127 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               0                4 
$`FAM8A1 MUTATED`
TCGA-2G-AAHA TCGA-4K-AAAL TCGA-XE-A8H4 
       98.53         4.83        18.38 

$`FAM8A1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        0.10        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        6.87        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
            4.83             0.10 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           98.53           229.22 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           18.38            38.30 
[1] "4.8 - 98.5 (18.4)"  "0.1 - 229.2 (38.3)"
[1] "hr="     "9200000"
D27V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM8A1 MUTATED         0        1        1        0         0         0
  FAM8A1 WILD-TYPE      19       23       10        5         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
                  vv
clus               STAGE IS
  FAM8A1 MUTATED          1
  FAM8A1 WILD-TYPE       45
D27V3, multiclass
            clus
vv           FAM8A1 MUTATED FAM8A1 WILD-TYPE
  STAGE I                 0               19
  STAGE IA                1               23
  STAGE IB                1               10
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 73 48  6
D27V4, multiclass
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2              127 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFZ       TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-2G-AAG5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGT       TCGA-2G-AAGV       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-AAH0 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAH2       TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL       TCGA-2G-AAHN 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD       TCGA-2G-AAKG 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM       TCGA-2G-AAL5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5       TCGA-2X-A9D6 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-S6-A8JW 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-S6-A8JX       TCGA-S6-A8JY       TCGA-SB-A6J6       TCGA-SB-A76C 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-SN-A6IS       TCGA-SN-A84W       TCGA-SN-A84X       TCGA-SN-A84Y 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-SO-A8JP       TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-VF-A8AC       TCGA-VF-A8AD       TCGA-VF-A8AE       TCGA-W4-A7U2 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-W4-A7U4       TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-WZ-A8D5       TCGA-X3-A8G4       TCGA-XE-A8H1       TCGA-XE-A8H5 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AANI       TCGA-XE-AANJ       TCGA-XE-AANR       TCGA-XE-AANV 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AAO3       TCGA-XE-AAO4       TCGA-XE-AAO6       TCGA-XE-AAOB 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AAOC       TCGA-XE-AAOD       TCGA-XE-AAOF       TCGA-XE-AAOJ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XE-AAOL       TCGA-XY-A89B       TCGA-XY-A8S2       TCGA-XY-A8S3 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-XY-A9T9       TCGA-YU-A90P       TCGA-YU-A90Q       TCGA-YU-A90S 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YU-A90W       TCGA-YU-A90Y       TCGA-YU-A912       TCGA-YU-A94D 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-YU-A94I       TCGA-YU-AA4L       TCGA-YU-AA61       TCGA-ZM-AA05 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-ZM-AA06       TCGA-ZM-AA0B       TCGA-ZM-AA0D       TCGA-ZM-AA0E 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
                  vv
clus               N0 N1+N2
  FAM8A1 MUTATED    1     0
  FAM8A1 WILD-TYPE 44    12
D27V5, multiclass
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               1               56 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-2G-AAG0       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" 
D27V6, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     3   0
  FAM8A1 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      3    0
  FAM8A1 WILD-TYPE  109    4
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM8A1 MUTATED       0                         0     3
  FAM8A1 WILD-TYPE     4                         6   112
D27V7, multiclass
                           clus
vv                          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D27V8, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     0   3
  FAM8A1 WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      0    3
  FAM8A1 WILD-TYPE   11  106
                        clus
vv                       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(28) Variable = SPTAN1 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  SPTAN1 MUTATED     3   0
  SPTAN1 WILD-TYPE 123   4
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               3              127 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               0                4 
$`SPTAN1 MUTATED`
TCGA-2G-AAGV TCGA-2G-AAH2 TCGA-SN-A84W 
      128.94        59.84         9.63 

$`SPTAN1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       60.26        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A6IS TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
       16.31        10.26        17.23         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
            9.63             0.10 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
          128.94           229.22 
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
           59.84            37.68 
[1] "9.6 - 128.9 (59.8)" "0.1 - 229.2 (37.7)"
[1] "hr="     "9200000"
D28V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTAN1 MUTATED         0        0        0        1         0         0
  SPTAN1 WILD-TYPE      19       24       11        4         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SPTAN1 MUTATED           0         0          0          0          0
  SPTAN1 WILD-TYPE         1         2          1          6          5
                  vv
clus               STAGE IS
  SPTAN1 MUTATED          2
  SPTAN1 WILD-TYPE       44
D28V3, multiclass
            clus
vv           SPTAN1 MUTATED SPTAN1 WILD-TYPE
  STAGE I                 0               19
  STAGE IA                0               24
  STAGE IB                0               11
  STAGE II                1                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
  STAGE IS                2               44
[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
  SPTAN1 MUTATED    2  1  0
  SPTAN1 WILD-TYPE 71 49  6
D28V4, multiclass
    clus
vv   SPTAN1 MUTATED SPTAN1 WILD-TYPE
  T1              2               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
  SPTAN1 MUTATED    1     0
  SPTAN1 WILD-TYPE 44    12
D28V5, multiclass
[1] "Remove cluster labels:" "SPTAN1 MUTATED"        
clus
  SPTAN1 MUTATED SPTAN1 WILD-TYPE 
               1               56 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAG0       TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAG8       TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAGE       TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAGJ       TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAGO       TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAHG 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAHL       TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-4K-AA1H       TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
      TCGA-VF-A8A8       TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" "SPTAN1 WILD-TYPE" 
D28V6, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     3   0
  SPTAN1 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      3    0
  SPTAN1 WILD-TYPE  109    4
   clus
vv  SPTAN1 MUTATED SPTAN1 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPTAN1 MUTATED       0                         0     3
  SPTAN1 WILD-TYPE     4                         6   112
D28V7, multiclass
                           clus
vv                          SPTAN1 MUTATED SPTAN1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D28V8, binary
                  cls
clus                 0   1
  SPTAN1 MUTATED     1   2
  SPTAN1 WILD-TYPE  10 107
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTAN1 MUTATED      1    2
  SPTAN1 WILD-TYPE   10  107
                        clus
vv                       SPTAN1 MUTATED SPTAN1 WILD-TYPE
  HISPANIC OR LATINO                  1               10
  NOT HISPANIC OR LATINO              2              107
[1] 2 2
[1] FALSE

Clustering(29) Variable = CRB2 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  CRB2 MUTATED     6   0
  CRB2 WILD-TYPE 120   4
  CRB2 MUTATED CRB2 WILD-TYPE 
             6            124 
  CRB2 MUTATED CRB2 WILD-TYPE 
             0              4 
$`CRB2 MUTATED`
TCGA-2G-AAF8 TCGA-2G-AAGK TCGA-2G-AAGX TCGA-S6-A8JY TCGA-YU-A912 TCGA-ZM-AA0B 
      122.40       108.16       170.33         9.14         5.29        27.55 

$`CRB2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAFG 
       20.32        30.35        38.30        59.70       102.35       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
      128.94        61.45        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       20.68        18.15        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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A94D 
       57.90        54.35        31.92        21.96         0.56        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D 
        7.96        40.96         8.15        37.02        39.35        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  CRB2 MUTATED CRB2 WILD-TYPE 
          5.29           0.10 
  CRB2 MUTATED CRB2 WILD-TYPE 
        170.33         229.22 
  CRB2 MUTATED CRB2 WILD-TYPE 
        67.855         37.990 
[1] "5.3 - 170.3 (67.9)" "0.1 - 229.2 (38.0)"
[1] "hr="     "2.6e+07"
D29V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRB2 MUTATED         0        3        0        0         0         0
  CRB2 WILD-TYPE      19       21       11        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  CRB2 MUTATED           0         0          0          0          1        2
  CRB2 WILD-TYPE         1         2          1          6          4       44
D29V3, multiclass
            clus
vv           CRB2 MUTATED CRB2 WILD-TYPE
  STAGE I               0             19
  STAGE IA              3             21
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              2             44
[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
  CRB2 MUTATED    5  1  0
  CRB2 WILD-TYPE 68 49  6
D29V4, multiclass
    clus
vv   CRB2 MUTATED CRB2 WILD-TYPE
  T1            5             68
  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
  CRB2 MUTATED    3     0
  CRB2 WILD-TYPE 42    12
D29V5, multiclass
       clus
vv      CRB2 MUTATED CRB2 WILD-TYPE
  N0               3             42
  N1+N2            0             12
[1] 2 2
[1] FALSE
D29V6, binary
                cls
clus               0   1
  CRB2 MUTATED     5   0
  CRB2 WILD-TYPE 107   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRB2 MUTATED      5    0
  CRB2 WILD-TYPE  107    4
   clus
vv  CRB2 MUTATED CRB2 WILD-TYPE
  0            5            107
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRB2 MUTATED       0                         1     5
  CRB2 WILD-TYPE     4                         5   110
D29V7, multiclass
                           clus
vv                          CRB2 MUTATED CRB2 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                                5            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"
D29V8, binary
                cls
clus               0   1
  CRB2 MUTATED     0   5
  CRB2 WILD-TYPE  11 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRB2 MUTATED      0    5
  CRB2 WILD-TYPE   11  104
                        clus
vv                       CRB2 MUTATED CRB2 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(30) Variable = OPLAH MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  OPLAH MUTATED     4   0
  OPLAH WILD-TYPE 122   4
  OPLAH MUTATED OPLAH WILD-TYPE 
              4             126 
  OPLAH MUTATED OPLAH WILD-TYPE 
              0               4 
$`OPLAH MUTATED`
TCGA-2G-AAGS TCGA-2G-AAGZ TCGA-2X-A9D6 TCGA-SB-A6J6 
       59.28        60.16         0.13        13.58 

$`OPLAH WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH0 
      124.57       128.94        61.45       170.33        80.94        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
       70.59         2.73         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS TCGA-SN-A84W 
       20.68        18.15         9.14         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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  OPLAH MUTATED OPLAH WILD-TYPE 
           0.13            0.10 
  OPLAH MUTATED OPLAH WILD-TYPE 
          60.16          229.22 
  OPLAH MUTATED OPLAH WILD-TYPE 
          36.43           37.99 
[1] "0.1 - 60.2 (36.4)"  "0.1 - 229.2 (38.0)"
[1] "hr="     "9200000"
D30V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPLAH MUTATED         1        1        0        0         0         0
  OPLAH WILD-TYPE      18       23       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  OPLAH MUTATED           0         0          1          1          0        0
  OPLAH WILD-TYPE         1         2          0          5          5       46
D30V3, multiclass
            clus
vv           OPLAH MUTATED OPLAH WILD-TYPE
  STAGE I                1              18
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               0              46
[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 70 49  6
D30V4, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  T1             3              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
  OPLAH MUTATED    0     2
  OPLAH WILD-TYPE 45    10
D30V5, multiclass
[1] "Remove cluster labels:" "OPLAH MUTATED"         
clus
  OPLAH MUTATED OPLAH WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D30V6, binary
                 cls
clus                0   1
  OPLAH MUTATED     3   1
  OPLAH WILD-TYPE 109   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      3    1
  OPLAH WILD-TYPE  109    3
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0             3             109
  1             1               3
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OPLAH MUTATED       0                         0     4
  OPLAH WILD-TYPE     4                         6   111
D30V7, multiclass
                           clus
vv                          OPLAH MUTATED OPLAH WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D30V8, binary
                 cls
clus                0   1
  OPLAH MUTATED     0   4
  OPLAH WILD-TYPE  11 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      0    4
  OPLAH WILD-TYPE   11  105
                        clus
vv                       OPLAH MUTATED OPLAH WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(31) Variable = GAS2L2 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  GAS2L2 MUTATED     3   0
  GAS2L2 WILD-TYPE 123   4
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               3              127 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               0                4 
$`GAS2L2 MUTATED`
TCGA-2G-AAFM TCGA-2G-AAHL TCGA-XE-AANI 
        9.57        59.80        34.22 

$`GAS2L2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN 
      191.31        36.99        14.14        14.56        17.16        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.74        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        6.87        18.38        40.01        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
            9.57             0.10 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
           59.80           229.22 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
           34.22            38.30 
[1] "9.6 - 59.8 (34.2)"  "0.1 - 229.2 (38.3)"
[1] "hr="     "9200000"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAS2L2 MUTATED         1        0        0        0         1         0
  GAS2L2 WILD-TYPE      18       24       11        5         4         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GAS2L2 MUTATED           0         0          0          0          0
  GAS2L2 WILD-TYPE         1         2          1          6          5
                  vv
clus               STAGE IS
  GAS2L2 MUTATED          1
  GAS2L2 WILD-TYPE       45
D31V3, multiclass
            clus
vv           GAS2L2 MUTATED GAS2L2 WILD-TYPE
  STAGE I                 1               18
  STAGE IA                0               24
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                1               45
[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
  GAS2L2 MUTATED    1  2  0
  GAS2L2 WILD-TYPE 72 48  6
D31V4, multiclass
    clus
vv   GAS2L2 MUTATED GAS2L2 WILD-TYPE
  T1              1               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
  GAS2L2 MUTATED    1     1
  GAS2L2 WILD-TYPE 44    11
D31V5, multiclass
[1] "Remove cluster labels:" "GAS2L2 MUTATED"        
clus
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               2               55 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFN 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAG0 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAG5       TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAG9       TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAGF       TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAGK       TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAGP       TCGA-2G-AAGS       TCGA-2G-AAGW       TCGA-2G-AAGX 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH2       TCGA-2G-AAHG 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKG 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-4K-AA1G       TCGA-4K-AA1H 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-4K-AA1I       TCGA-4K-AAAL       TCGA-SO-A8JP       TCGA-VF-A8A8 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
      TCGA-VF-A8AA       TCGA-VF-A8AB       TCGA-X3-A8G4 
"GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" "GAS2L2 WILD-TYPE" 
D31V6, binary
                  cls
clus                 0   1
  GAS2L2 MUTATED     3   0
  GAS2L2 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      3    0
  GAS2L2 WILD-TYPE  109    4
   clus
vv  GAS2L2 MUTATED GAS2L2 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAS2L2 MUTATED       0                         0     3
  GAS2L2 WILD-TYPE     4                         6   112
D31V7, multiclass
                           clus
vv                          GAS2L2 MUTATED GAS2L2 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D31V8, binary
                  cls
clus                 0   1
  GAS2L2 MUTATED     0   3
  GAS2L2 WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      0    3
  GAS2L2 WILD-TYPE   11  106
                        clus
vv                       GAS2L2 MUTATED GAS2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(32) Variable = CDC27 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED     6   0
  CDC27 WILD-TYPE 120   4
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             124 
  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 
       30.35        36.99        63.22       176.15         0.10         0.43 

$`CDC27 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       72.20        61.71        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       79.76        67.96        92.09        75.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       59.80        91.43         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX 
        0.13         3.52         7.00         4.83        20.68        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         3.52        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         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I 
       31.92        21.96         0.56         5.29        58.88         7.96 
TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       40.96         8.15        37.02        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.10            0.13 
  CDC27 MUTATED CDC27 WILD-TYPE 
         176.15          229.22 
  CDC27 MUTATED CDC27 WILD-TYPE 
         33.670          38.825 
[1] "0.1 - 176.2 (33.7)" "0.1 - 229.2 (38.8)"
[1] "hr="     "2.6e+07"
D32V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC27 MUTATED         1        1        1        0         0         1
  CDC27 WILD-TYPE      18       23       10        5         5         0
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  CDC27 MUTATED           0         0          0          0          0        2
  CDC27 WILD-TYPE         1         2          1          6          5       44
D32V3, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                1              18
  STAGE IA               1              23
  STAGE IB               1              10
  STAGE II               0               5
  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
  STAGE IS               2              44
[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 69 48  6
D32V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             4              69
  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
D32V5, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  N0                4              41
  N1+N2             1              11
[1] 2 2
[1] FALSE
D32V6, binary
                 cls
clus                0   1
  CDC27 MUTATED     6   0
  CDC27 WILD-TYPE 106   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      6    0
  CDC27 WILD-TYPE  106    4
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             6             106
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         1     5
  CDC27 WILD-TYPE     4                         5   110
D32V7, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 5             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"
D32V8, binary
                 cls
clus                0   1
  CDC27 MUTATED     0   6
  CDC27 WILD-TYPE  11 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    6
  CDC27 WILD-TYPE   11  103
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             6             103
[1] 2 2
[1] FALSE

Clustering(33) Variable = MUC2 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  MUC2 MUTATED    14   0
  MUC2 WILD-TYPE 112   4
  MUC2 MUTATED MUC2 WILD-TYPE 
            14            116 
  MUC2 MUTATED MUC2 WILD-TYPE 
             0              4 
$`MUC2 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAG0 TCGA-2G-AAGA TCGA-2G-AAGS TCGA-2G-AAGX 
       30.35        59.70        40.01        68.22        59.28       170.33 
TCGA-2G-AAH4 TCGA-2G-AAHN TCGA-2G-AAKD TCGA-SO-A8JP TCGA-VF-A8AB TCGA-XE-A8H4 
      125.69        91.43       122.50         3.52        24.99        18.38 
TCGA-XE-AANR TCGA-YU-A94I 
        0.46         7.96 

$`MUC2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       20.32        38.30       102.35       122.40       191.31        36.99 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       40.70        36.13        36.89        52.37        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       61.71        63.22        63.32        72.85        68.38        79.76 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN 
       67.96        92.09        75.09       108.16        59.64       106.39 
TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY 
      115.00       120.62       124.57       128.94        61.45        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.16        60.26        59.84        59.90        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKG 
       59.74        59.80        59.80       176.15         6.08       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AC 
        9.63        10.26        17.23        37.18        37.68        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         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.16         0.82        28.14         6.87        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
       65.98        53.03        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         8.32 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S 
       12.92        20.12         6.90        57.90        54.35        31.92 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 
       21.96         0.56         5.29        58.88        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       46.88        10.85 

  MUC2 MUTATED MUC2 WILD-TYPE 
          0.46           0.10 
  MUC2 MUTATED MUC2 WILD-TYPE 
        170.33         229.22 
  MUC2 MUTATED MUC2 WILD-TYPE 
        49.645         37.430 
[1] "0.5 - 170.3 (49.6)" "0.1 - 229.2 (37.4)"
[1] "hr="   "8e+07"
D33V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC2 MUTATED         4        4        0        1         1         0
  MUC2 WILD-TYPE      15       20       11        4         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  MUC2 MUTATED           0         1          0          1          0        2
  MUC2 WILD-TYPE         1         1          1          5          5       44
D33V3, multiclass
            clus
vv           MUC2 MUTATED MUC2 WILD-TYPE
  STAGE I               4             15
  STAGE IA              4             20
  STAGE IB              0             11
  STAGE II              1              4
  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
  STAGE IS              2             44
[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 63 47  6
D33V4, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  T1           10             63
  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 99  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     13    0
  MUC2 WILD-TYPE   99    4
   clus
vv  MUC2 MUTATED MUC2 WILD-TYPE
  0           13             99
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC2 MUTATED       0                         1    12
  MUC2 WILD-TYPE     4                         5   103
D33V7, multiclass
                           clus
vv                          MUC2 MUTATED MUC2 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                               12            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                cls
clus              0  1
  MUC2 MUTATED    1 12
  MUC2 WILD-TYPE 10 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED      1   12
  MUC2 WILD-TYPE   10   97
                        clus
vv                       MUC2 MUTATED MUC2 WILD-TYPE
  HISPANIC OR LATINO                1             10
  NOT HISPANIC OR LATINO           12             97
[1] 2 2
[1] FALSE

Clustering(34) Variable = TPTE2 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED     4   0
  TPTE2 WILD-TYPE 122   4
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4             126 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              0               4 
$`TPTE2 MUTATED`
TCGA-2G-AAHA TCGA-SB-A76C TCGA-SO-A8JP TCGA-XE-A8H4 
       98.53         1.38         3.52        18.38 

$`TPTE2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
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-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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           1.38            0.10 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          98.53          229.22 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
         10.950          38.825 
[1] "1.4 - 98.5 (10.9)"  "0.1 - 229.2 (38.8)"
[1] "hr="     "9300000"
D34V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPTE2 MUTATED         1        1        1        0         0         0
  TPTE2 WILD-TYPE      18       23       10        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  TPTE2 MUTATED           0         0          0          0          0        0
  TPTE2 WILD-TYPE         1         2          1          6          5       46
D34V3, multiclass
            clus
vv           TPTE2 MUTATED TPTE2 WILD-TYPE
  STAGE I                1              18
  STAGE IA               1              23
  STAGE IB               1              10
  STAGE II               0               5
  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
  STAGE IS               0              46
[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 71 49  6
D34V4, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  T1             2              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
  TPTE2 MUTATED    1     0
  TPTE2 WILD-TYPE 44    12
D34V5, multiclass
[1] "Remove cluster labels:" "TPTE2 MUTATED"         
clus
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              1              56 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D34V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED     4   0
  TPTE2 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      4    0
  TPTE2 WILD-TYPE  108    4
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED       0                         0     4
  TPTE2 WILD-TYPE     4                         6   111
D34V7, multiclass
                           clus
vv                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D34V8, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0   4
  TPTE2 WILD-TYPE  11 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0    4
  TPTE2 WILD-TYPE   11  105
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(35) Variable = NAT10 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  NAT10 MUTATED     4   0
  NAT10 WILD-TYPE 122   4
  NAT10 MUTATED NAT10 WILD-TYPE 
              4             126 
  NAT10 MUTATED NAT10 WILD-TYPE 
              0               4 
$`NAT10 MUTATED`
TCGA-2G-AAGM TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-VF-A8A8 
       59.64        13.58        16.31        37.18 

$`NAT10 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
       75.09       108.16       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C 
        0.10         4.83        20.68        18.15         9.14         1.38 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB 
        9.63        10.26        17.23         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  NAT10 MUTATED NAT10 WILD-TYPE 
          13.58            0.10 
  NAT10 MUTATED NAT10 WILD-TYPE 
          59.64          229.22 
  NAT10 MUTATED NAT10 WILD-TYPE 
         26.745          38.825 
[1] "13.6 - 59.6 (26.7)" "0.1 - 229.2 (38.8)"
[1] "hr="     "2.5e+07"
D35V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAT10 MUTATED         0        2        0        0         0         0
  NAT10 WILD-TYPE      19       22       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  NAT10 MUTATED           0         0          0          0          0        2
  NAT10 WILD-TYPE         1         2          1          6          5       44
D35V3, multiclass
            clus
vv           NAT10 MUTATED NAT10 WILD-TYPE
  STAGE I                0              19
  STAGE IA               2              22
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               2              44
[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 70 49  6
D35V4, multiclass
    clus
vv   NAT10 MUTATED NAT10 WILD-TYPE
  T1             3              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
  NAT10 MUTATED    2     0
  NAT10 WILD-TYPE 43    12
D35V5, multiclass
[1] "Remove cluster labels:" "NAT10 MUTATED"         
clus
  NAT10 MUTATED NAT10 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" "NAT10 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D35V6, binary
                 cls
clus                0   1
  NAT10 MUTATED     4   0
  NAT10 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAT10 MUTATED      4    0
  NAT10 WILD-TYPE  108    4
   clus
vv  NAT10 MUTATED NAT10 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAT10 MUTATED       0                         0     4
  NAT10 WILD-TYPE     4                         6   111
D35V7, multiclass
                           clus
vv                          NAT10 MUTATED NAT10 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D35V8, binary
                 cls
clus                0   1
  NAT10 MUTATED     1   3
  NAT10 WILD-TYPE  10 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAT10 MUTATED      1    3
  NAT10 WILD-TYPE   10  106
                        clus
vv                       NAT10 MUTATED NAT10 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(36) Variable = INTS4 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  INTS4 MUTATED     3   0
  INTS4 WILD-TYPE 123   4
  INTS4 MUTATED INTS4 WILD-TYPE 
              3             127 
  INTS4 MUTATED INTS4 WILD-TYPE 
              0               4 
$`INTS4 MUTATED`
TCGA-XE-A8H5 TCGA-XE-AAOD TCGA-XY-A8S2 
       40.01        67.66        12.92 

$`INTS4 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANI TCGA-XE-AANJ 
        0.82        28.14         6.87        18.38        34.22        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB 
        0.46        53.03        93.93        12.07         7.89        16.87 
TCGA-XE-AAOC TCGA-XE-AAOF TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S3 
        8.88        41.69        50.96         0.43         8.32        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  INTS4 MUTATED INTS4 WILD-TYPE 
          12.92            0.10 
  INTS4 MUTATED INTS4 WILD-TYPE 
          67.66          229.22 
  INTS4 MUTATED INTS4 WILD-TYPE 
          40.01           37.68 
[1] "12.9 - 67.7 (40.0)" "0.1 - 229.2 (37.7)"
[1] "hr="     "9200000"
D36V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INTS4 MUTATED         1        0        1        0         0         0
  INTS4 WILD-TYPE      18       24       10        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  INTS4 MUTATED           0         0          0          0          0        1
  INTS4 WILD-TYPE         1         2          1          6          5       45
D36V3, multiclass
            clus
vv           INTS4 MUTATED INTS4 WILD-TYPE
  STAGE I                1              18
  STAGE IA               0              24
  STAGE IB               1              10
  STAGE II               0               5
  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
  STAGE IS               1              45
[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
  INTS4 MUTATED    1  2  0
  INTS4 WILD-TYPE 72 48  6
D36V4, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  T1             1              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
  INTS4 MUTATED    0     0
  INTS4 WILD-TYPE 45    12
D36V5, multiclass
D36V6, binary
                 cls
clus                0   1
  INTS4 MUTATED     3   0
  INTS4 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED      3    0
  INTS4 WILD-TYPE  109    4
   clus
vv  INTS4 MUTATED INTS4 WILD-TYPE
  0             3             109
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INTS4 MUTATED       0                         0     2
  INTS4 WILD-TYPE     4                         6   113
D36V7, multiclass
[1] "Remove cluster labels:" "INTS4 MUTATED"         
clus
  INTS4 MUTATED INTS4 WILD-TYPE 
              2             123 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAFZ      TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-2G-AAG5 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8      TCGA-2G-AAG9 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE      TCGA-2G-AAGF 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGT      TCGA-2G-AAGV      TCGA-2G-AAGW 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH0 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAH2      TCGA-2G-AAH3      TCGA-2G-AAH4      TCGA-2G-AAH8 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAHA      TCGA-2G-AAHC      TCGA-2G-AAHG      TCGA-2G-AAHL 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKD 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAKH      TCGA-2G-AAKL      TCGA-2G-AAKM 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-2G-AALP      TCGA-2X-A9D5 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-2X-A9D6      TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AA1I 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-4K-AAAL      TCGA-S6-A8JW      TCGA-S6-A8JX      TCGA-S6-A8JY 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-SB-A6J6      TCGA-SB-A76C      TCGA-SN-A6IS      TCGA-SN-A84W 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-SN-A84X      TCGA-SN-A84Y      TCGA-SO-A8JP      TCGA-VF-A8A8 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-VF-A8AC      TCGA-VF-A8AD 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-VF-A8AE      TCGA-W4-A7U2      TCGA-W4-A7U4      TCGA-WZ-A7V3 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-WZ-A7V4      TCGA-WZ-A7V5      TCGA-WZ-A8D5      TCGA-X3-A8G4 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-XE-A8H1      TCGA-XE-A8H4      TCGA-XE-AANI      TCGA-XE-AANJ 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-XE-AANR      TCGA-XE-AAO3      TCGA-XE-AAO4      TCGA-XE-AAO6 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-XE-AAOB      TCGA-XE-AAOC      TCGA-XE-AAOF      TCGA-XE-AAOJ 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-XE-AAOL      TCGA-XY-A89B      TCGA-XY-A8S3      TCGA-XY-A9T9 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-YU-A90P      TCGA-YU-A90S      TCGA-YU-A90W      TCGA-YU-A90Y 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-YU-A912      TCGA-YU-AA4L      TCGA-YU-AA61      TCGA-ZM-AA05 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-ZM-AA06      TCGA-ZM-AA0B      TCGA-ZM-AA0D      TCGA-ZM-AA0E 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
     TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"INTS4 WILD-TYPE" "INTS4 WILD-TYPE" "INTS4 WILD-TYPE" 
D36V8, binary
                 cls
clus                0   1
  INTS4 MUTATED     1   2
  INTS4 WILD-TYPE  10 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED      1    2
  INTS4 WILD-TYPE   10  107
                        clus
vv                       INTS4 MUTATED INTS4 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(37) Variable = TTC38 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  TTC38 MUTATED     4   0
  TTC38 WILD-TYPE 122   4
  TTC38 MUTATED TTC38 WILD-TYPE 
              4             126 
  TTC38 MUTATED TTC38 WILD-TYPE 
              0               4 
$`TTC38 MUTATED`
TCGA-2G-AAEX TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAH8 
       30.35        67.96        92.09        61.84 

$`TTC38 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       72.85        68.38        79.76        75.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90       125.69        98.53        59.74        59.80        59.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       91.43       176.15         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  TTC38 MUTATED TTC38 WILD-TYPE 
          30.35            0.10 
  TTC38 MUTATED TTC38 WILD-TYPE 
          92.09          229.22 
  TTC38 MUTATED TTC38 WILD-TYPE 
          64.90           37.43 
[1] "30.4 - 92.1 (64.9)" "0.1 - 229.2 (37.4)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTC38 MUTATED         0        0        0        0         0         0
  TTC38 WILD-TYPE      19       24       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  TTC38 MUTATED           0         0          0          0          2        2
  TTC38 WILD-TYPE         1         2          1          6          3       44
D37V3, multiclass
            clus
vv           TTC38 MUTATED TTC38 WILD-TYPE
  STAGE I                0              19
  STAGE IA               0              24
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               2              44
[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 71 49  5
D37V4, multiclass
    clus
vv   TTC38 MUTATED TTC38 WILD-TYPE
  T1             2              71
  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
D37V5, multiclass
       clus
vv      TTC38 MUTATED TTC38 WILD-TYPE
  N0                2              43
  N1+N2             1              11
[1] 2 2
[1] FALSE
D37V6, binary
                 cls
clus                0   1
  TTC38 MUTATED     3   1
  TTC38 WILD-TYPE 109   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC38 MUTATED      3    1
  TTC38 WILD-TYPE  109    3
   clus
vv  TTC38 MUTATED TTC38 WILD-TYPE
  0             3             109
  1             1               3
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTC38 MUTATED       0                         0     4
  TTC38 WILD-TYPE     4                         6   111
D37V7, multiclass
                           clus
vv                          TTC38 MUTATED TTC38 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D37V8, binary
                 cls
clus                0   1
  TTC38 MUTATED     0   4
  TTC38 WILD-TYPE  11 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC38 MUTATED      0    4
  TTC38 WILD-TYPE   11  105
                        clus
vv                       TTC38 MUTATED TTC38 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(38) Variable = RBM3 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  RBM3 MUTATED     3   0
  RBM3 WILD-TYPE 123   4
  RBM3 MUTATED RBM3 WILD-TYPE 
             3            127 
  RBM3 MUTATED RBM3 WILD-TYPE 
             0              4 
$`RBM3 MUTATED`
TCGA-2G-AAKD TCGA-WZ-A7V3 TCGA-ZM-AA06 
      122.50         3.65        39.35 

$`RBM3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
        6.08       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 
       41.52        24.26         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  RBM3 MUTATED RBM3 WILD-TYPE 
          3.65           0.10 
  RBM3 MUTATED RBM3 WILD-TYPE 
        122.50         229.22 
  RBM3 MUTATED RBM3 WILD-TYPE 
         39.35          37.68 
[1] "3.6 - 122.5 (39.4)" "0.1 - 229.2 (37.7)"
[1] "hr="     "9200000"
D38V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM3 MUTATED         1        0        1        0         0         0
  RBM3 WILD-TYPE      18       24       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RBM3 MUTATED           0         1          0          0          0        0
  RBM3 WILD-TYPE         1         1          1          6          5       46
D38V3, multiclass
            clus
vv           RBM3 MUTATED RBM3 WILD-TYPE
  STAGE I               1             18
  STAGE IA              0             24
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              0             46
[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 72 48  6
D38V4, multiclass
    clus
vv   RBM3 MUTATED RBM3 WILD-TYPE
  T1            1             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
  RBM3 MUTATED    0     0
  RBM3 WILD-TYPE 45    12
D38V5, multiclass
D38V6, binary
                cls
clus               0   1
  RBM3 MUTATED     2   0
  RBM3 WILD-TYPE 110   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM3 MUTATED      2    0
  RBM3 WILD-TYPE  110    4
   clus
vv  RBM3 MUTATED RBM3 WILD-TYPE
  0            2            110
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM3 MUTATED       0                         0     3
  RBM3 WILD-TYPE     4                         6   112
D38V7, multiclass
                           clus
vv                          RBM3 MUTATED RBM3 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            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"
D38V8, binary
                cls
clus               0   1
  RBM3 MUTATED     0   3
  RBM3 WILD-TYPE  11 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM3 MUTATED      0    3
  RBM3 WILD-TYPE   11  106
                        clus
vv                       RBM3 MUTATED RBM3 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            3            106
[1] 2 2
[1] FALSE

Clustering(39) Variable = TCHH MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  TCHH MUTATED     5   0
  TCHH WILD-TYPE 121   4
  TCHH MUTATED TCHH WILD-TYPE 
             5            125 
  TCHH MUTATED TCHH WILD-TYPE 
             0              4 
$`TCHH MUTATED`
TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAGJ TCGA-XE-AAOF TCGA-YU-A90S 
       36.99        63.32        75.09        41.69        31.92 

$`TCHH WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC 
       71.24        72.20        61.71        63.22        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       68.38        79.76        67.96        92.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       57.90        54.35        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  TCHH MUTATED TCHH WILD-TYPE 
         31.92           0.10 
  TCHH MUTATED TCHH WILD-TYPE 
         75.09         229.22 
  TCHH MUTATED TCHH WILD-TYPE 
         41.69          37.68 
[1] "31.9 - 75.1 (41.7)" "0.1 - 229.2 (37.7)"
[1] "hr="     "2.6e+07"
D39V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCHH MUTATED         0        3        0        0         0         1
  TCHH WILD-TYPE      19       21       11        5         5         0
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  TCHH MUTATED           0         0          0          1          0        0
  TCHH WILD-TYPE         1         2          1          5          5       46
D39V3, multiclass
            clus
vv           TCHH MUTATED TCHH WILD-TYPE
  STAGE I               0             19
  STAGE IA              3             21
  STAGE IB              0             11
  STAGE II              0              5
  STAGE IIA             0              5
  STAGE IIB             1              0
  STAGE IIC             0              1
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            1              5
  STAGE IIIC            0              5
  STAGE IS              0             46
[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
  TCHH MUTATED    4  1  0
  TCHH WILD-TYPE 69 49  6
D39V4, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  T1            4             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
  TCHH MUTATED    1     2
  TCHH WILD-TYPE 44    10
D39V5, multiclass
       clus
vv      TCHH MUTATED TCHH WILD-TYPE
  N0               1             44
  N1+N2            2             10
[1] 2 2
[1] FALSE
D39V6, binary
                cls
clus               0   1
  TCHH MUTATED     4   0
  TCHH WILD-TYPE 108   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      4    0
  TCHH WILD-TYPE  108    4
   clus
vv  TCHH MUTATED TCHH WILD-TYPE
  0            4            108
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCHH MUTATED       1                         1     3
  TCHH WILD-TYPE     3                         5   112
D39V7, multiclass
                           clus
vv                          TCHH MUTATED TCHH WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                                3            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"
D39V8, binary
                cls
clus               0   1
  TCHH MUTATED     0   4
  TCHH WILD-TYPE  11 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      0    4
  TCHH WILD-TYPE   11  105
                        clus
vv                       TCHH MUTATED TCHH WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            105
[1] 2 2
[1] FALSE

Clustering(40) Variable = ZC3H11A MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  ZC3H11A MUTATED     3   0
  ZC3H11A WILD-TYPE 123   4
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               127 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                0                 4 
$`ZC3H11A MUTATED`
TCGA-YU-A90S TCGA-YU-AA4L TCGA-ZM-AA05 
       31.92        40.96        37.02 

$`ZC3H11A WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        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 
        8.32        12.92        20.12         6.90        57.90        54.35 
TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 
       21.96         0.56         5.29        58.88         7.96         8.15 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            31.92              0.10 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            40.96            229.22 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            37.02             38.30 
[1] "31.9 - 41.0 (37.0)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.5e+07"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H11A MUTATED         0        1        0        0         0         0
  ZC3H11A WILD-TYPE      19       23       11        5         5         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZC3H11A MUTATED           1         0          0          0          1
  ZC3H11A WILD-TYPE         0         2          1          6          4
                   vv
clus                STAGE IS
  ZC3H11A MUTATED          0
  ZC3H11A WILD-TYPE       46
D40V3, multiclass
            clus
vv           ZC3H11A MUTATED ZC3H11A WILD-TYPE
  STAGE I                  0                19
  STAGE IA                 1                23
  STAGE IB                 0                11
  STAGE II                 0                 5
  STAGE IIA                0                 5
  STAGE IIB                0                 1
  STAGE IIC                1                 0
  STAGE III                0                 2
  STAGE IIIA               0                 1
  STAGE IIIB               0                 6
  STAGE IIIC               1                 4
  STAGE IS                 0                46
[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
  ZC3H11A MUTATED    2  1  0
  ZC3H11A WILD-TYPE 71 49  6
D40V4, multiclass
    clus
vv   ZC3H11A MUTATED ZC3H11A WILD-TYPE
  T1               2                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
  ZC3H11A MUTATED    0     0
  ZC3H11A WILD-TYPE 45    12
D40V5, multiclass
D40V6, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     1   0
  ZC3H11A WILD-TYPE 111   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      1    0
  ZC3H11A WILD-TYPE  111    4
   clus
vv  ZC3H11A MUTATED ZC3H11A WILD-TYPE
  0               1               111
  1               0                 4
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H11A MUTATED       0                         1     2
  ZC3H11A WILD-TYPE     4                         5   113
D40V7, multiclass
                           clus
vv                          ZC3H11A MUTATED ZC3H11A WILD-TYPE
  ASIAN                                   0                 4
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   2               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"
D40V8, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     0   1
  ZC3H11A WILD-TYPE  11 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      0    1
  ZC3H11A WILD-TYPE   11  108
                        clus
vv                       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               1               108
[1] 2 2
[1] FALSE

Clustering(41) Variable = RAC1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  RAC1 MUTATED     4   0
  RAC1 WILD-TYPE 122   4
  RAC1 MUTATED RAC1 WILD-TYPE 
             4            126 
  RAC1 MUTATED RAC1 WILD-TYPE 
             0              4 
$`RAC1 MUTATED`
TCGA-2G-AAHT TCGA-2G-AAL7 TCGA-4K-AAAL TCGA-XE-AANV 
        6.08       131.21         4.83        53.03 

$`RAC1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 
       18.38        40.01        34.22        65.98         0.46        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  RAC1 MUTATED RAC1 WILD-TYPE 
          4.83           0.10 
  RAC1 MUTATED RAC1 WILD-TYPE 
        131.21         229.22 
  RAC1 MUTATED RAC1 WILD-TYPE 
        29.555         37.990 
[1] "4.8 - 131.2 (29.6)" "0.1 - 229.2 (38.0)"
[1] "hr="     "2.5e+07"
D41V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAC1 MUTATED         0        0        1        0         0         0
  RAC1 WILD-TYPE      19       24       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RAC1 MUTATED           0         0          0          0          0        3
  RAC1 WILD-TYPE         1         2          1          6          5       43
D41V3, multiclass
            clus
vv           RAC1 MUTATED RAC1 WILD-TYPE
  STAGE I               0             19
  STAGE IA              0             24
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              3             43
[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 73 46  6
D41V4, multiclass
    clus
vv   RAC1 MUTATED RAC1 WILD-TYPE
  T1            0             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
  RAC1 MUTATED    3     0
  RAC1 WILD-TYPE 42    12
D41V5, multiclass
       clus
vv      RAC1 MUTATED RAC1 WILD-TYPE
  N0               3             42
  N1+N2            0             12
[1] 2 2
[1] FALSE
D41V6, binary
                cls
clus               0   1
  RAC1 MUTATED     4   0
  RAC1 WILD-TYPE 108   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      4    0
  RAC1 WILD-TYPE  108    4
   clus
vv  RAC1 MUTATED RAC1 WILD-TYPE
  0            4            108
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAC1 MUTATED       0                         0     3
  RAC1 WILD-TYPE     4                         6   112
D41V7, multiclass
                           clus
vv                          RAC1 MUTATED RAC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            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"
D41V8, binary
                cls
clus               0   1
  RAC1 MUTATED     0   4
  RAC1 WILD-TYPE  11 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      0    4
  RAC1 WILD-TYPE   11  105
                        clus
vv                       RAC1 MUTATED RAC1 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            105
[1] 2 2
[1] FALSE

Clustering(42) Variable = MTIF3 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  MTIF3 MUTATED     3   0
  MTIF3 WILD-TYPE 123   4
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              3             127 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              0               4 
$`MTIF3 MUTATED`
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-ZM-AA0D 
       40.01        34.22        17.39 

$`MTIF3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANJ TCGA-XE-AANR 
        0.82        28.14         6.87        18.38        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  MTIF3 MUTATED MTIF3 WILD-TYPE 
          17.39            0.10 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
          40.01          229.22 
  MTIF3 MUTATED MTIF3 WILD-TYPE 
          34.22           38.30 
[1] "17.4 - 40.0 (34.2)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.5e+07"
D42V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTIF3 MUTATED         0        1        0        0         0         0
  MTIF3 WILD-TYPE      19       23       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  MTIF3 MUTATED           0         0          0          0          0        2
  MTIF3 WILD-TYPE         1         2          1          6          5       44
D42V3, multiclass
            clus
vv           MTIF3 MUTATED MTIF3 WILD-TYPE
  STAGE I                0              19
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               2              44
[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 70 50  6
D42V4, multiclass
    clus
vv   MTIF3 MUTATED MTIF3 WILD-TYPE
  T1             3              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
  MTIF3 MUTATED    0     0
  MTIF3 WILD-TYPE 45    12
D42V5, multiclass
D42V6, binary
                 cls
clus                0   1
  MTIF3 MUTATED     3   0
  MTIF3 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF3 MUTATED      3    0
  MTIF3 WILD-TYPE  109    4
   clus
vv  MTIF3 MUTATED MTIF3 WILD-TYPE
  0             3             109
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTIF3 MUTATED       0                         0     2
  MTIF3 WILD-TYPE     4                         6   113
D42V7, multiclass
[1] "Remove cluster labels:" "MTIF3 MUTATED"         
clus
  MTIF3 MUTATED MTIF3 WILD-TYPE 
              2             123 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAFZ      TCGA-2G-AAG0      TCGA-2G-AAG3      TCGA-2G-AAG5 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAG6      TCGA-2G-AAG7      TCGA-2G-AAG8      TCGA-2G-AAG9 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGA      TCGA-2G-AAGC      TCGA-2G-AAGE      TCGA-2G-AAGF 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGG      TCGA-2G-AAGI      TCGA-2G-AAGJ      TCGA-2G-AAGK 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGM      TCGA-2G-AAGN      TCGA-2G-AAGO      TCGA-2G-AAGP 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGS      TCGA-2G-AAGT      TCGA-2G-AAGV      TCGA-2G-AAGW 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAGX      TCGA-2G-AAGY      TCGA-2G-AAGZ      TCGA-2G-AAH0 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAH2      TCGA-2G-AAH3      TCGA-2G-AAH4      TCGA-2G-AAH8 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAHA      TCGA-2G-AAHC      TCGA-2G-AAHG      TCGA-2G-AAHL 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAHN      TCGA-2G-AAHP      TCGA-2G-AAHT      TCGA-2G-AAKD 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAKG      TCGA-2G-AAKH      TCGA-2G-AAKL      TCGA-2G-AAKM 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2G-AAL5      TCGA-2G-AAL7      TCGA-2G-AALP      TCGA-2X-A9D5 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-2X-A9D6      TCGA-4K-AA1G      TCGA-4K-AA1H      TCGA-4K-AA1I 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-4K-AAAL      TCGA-S6-A8JW      TCGA-S6-A8JX      TCGA-S6-A8JY 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-SB-A6J6      TCGA-SB-A76C      TCGA-SN-A6IS      TCGA-SN-A84W 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-SN-A84X      TCGA-SN-A84Y      TCGA-SO-A8JP      TCGA-VF-A8A8 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-VF-A8AA      TCGA-VF-A8AB      TCGA-VF-A8AC      TCGA-VF-A8AD 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-VF-A8AE      TCGA-W4-A7U2      TCGA-W4-A7U4      TCGA-WZ-A7V3 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-WZ-A7V4      TCGA-WZ-A7V5      TCGA-WZ-A8D5      TCGA-X3-A8G4 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-A8H1      TCGA-XE-A8H4      TCGA-XE-AANJ      TCGA-XE-AANR 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AAO3      TCGA-XE-AAO4      TCGA-XE-AAO6      TCGA-XE-AAOB 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AAOC      TCGA-XE-AAOD      TCGA-XE-AAOF      TCGA-XE-AAOJ 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XE-AAOL      TCGA-XY-A89B      TCGA-XY-A8S2      TCGA-XY-A8S3 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-XY-A9T9      TCGA-YU-A90P      TCGA-YU-A90S      TCGA-YU-A90W 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-YU-A90Y      TCGA-YU-A912      TCGA-YU-AA4L      TCGA-YU-AA61 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-ZM-AA05      TCGA-ZM-AA06      TCGA-ZM-AA0B      TCGA-ZM-AA0E 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
     TCGA-ZM-AA0F      TCGA-ZM-AA0H      TCGA-ZM-AA0N 
"MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" "MTIF3 WILD-TYPE" 
D42V8, binary
                 cls
clus                0   1
  MTIF3 MUTATED     1   2
  MTIF3 WILD-TYPE  10 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF3 MUTATED      1    2
  MTIF3 WILD-TYPE   10  107
                        clus
vv                       MTIF3 MUTATED MTIF3 WILD-TYPE
  HISPANIC OR LATINO                 1              10
  NOT HISPANIC OR LATINO             2             107
[1] 2 2
[1] FALSE

Clustering(43) Variable = MFF MUTATION ANALYSIS
D43V1, survival
               sevent
clus2             0   1
  MFF MUTATED     3   0
  MFF WILD-TYPE 123   4
  MFF MUTATED MFF WILD-TYPE 
            3           127 
  MFF MUTATED MFF WILD-TYPE 
            0             4 
$`MFF MUTATED`
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-W4-A7U2 
       37.18        37.68        41.52 

$`MFF WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE TCGA-W4-A7U4 
        3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  MFF MUTATED MFF WILD-TYPE 
        37.18          0.10 
  MFF MUTATED MFF WILD-TYPE 
        41.52        229.22 
  MFF MUTATED MFF WILD-TYPE 
        37.68         38.30 
[1] "37.2 - 41.5 (37.7)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.5e+07"
D43V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFF MUTATED         1        1        0        0         0         0
  MFF WILD-TYPE      18       23       11        5         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  MFF MUTATED           0         0          0          0          0        0
  MFF WILD-TYPE         1         2          1          6          5       46
D43V3, multiclass
[1] "Remove cluster labels:" "MFF MUTATED"           
clus
  MFF MUTATED MFF WILD-TYPE 
            2           124 
   TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4    TCGA-2G-AAF6 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFI    TCGA-2G-AAFJ 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAFY    TCGA-2G-AAFZ    TCGA-2G-AAG0    TCGA-2G-AAG3    TCGA-2G-AAG5 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAG6    TCGA-2G-AAG7    TCGA-2G-AAG8    TCGA-2G-AAG9    TCGA-2G-AAGA 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGC    TCGA-2G-AAGE    TCGA-2G-AAGF    TCGA-2G-AAGG    TCGA-2G-AAGI 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGJ    TCGA-2G-AAGK    TCGA-2G-AAGM    TCGA-2G-AAGN    TCGA-2G-AAGO 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGP    TCGA-2G-AAGS    TCGA-2G-AAGT    TCGA-2G-AAGV    TCGA-2G-AAGW 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGX    TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH0    TCGA-2G-AAH2 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAH3    TCGA-2G-AAH4    TCGA-2G-AAH8    TCGA-2G-AAHA    TCGA-2G-AAHC 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAHG    TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAKD    TCGA-2G-AAKG    TCGA-2G-AAKH    TCGA-2G-AAKL    TCGA-2G-AAKM 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAL5    TCGA-2G-AAL7    TCGA-2G-AALP    TCGA-2X-A9D5    TCGA-2X-A9D6 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-4K-AA1G    TCGA-4K-AA1H    TCGA-4K-AA1I    TCGA-4K-AAAL    TCGA-S6-A8JW 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-S6-A8JX    TCGA-S6-A8JY    TCGA-SB-A6J6    TCGA-SN-A6IS    TCGA-SN-A84W 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-SN-A84X    TCGA-SN-A84Y    TCGA-SO-A8JP    TCGA-VF-A8AB    TCGA-VF-A8AC 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-VF-A8AD    TCGA-VF-A8AE    TCGA-WZ-A7V3    TCGA-WZ-A7V4    TCGA-WZ-A7V5 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-X3-A8G4    TCGA-XE-A8H1    TCGA-XE-A8H4    TCGA-XE-A8H5    TCGA-XE-AANI 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-XE-AANJ    TCGA-XE-AANR    TCGA-XE-AANV    TCGA-XE-AAO3    TCGA-XE-AAO4 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-XE-AAO6    TCGA-XE-AAOB    TCGA-XE-AAOC    TCGA-XE-AAOD    TCGA-XE-AAOF 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-XE-AAOJ    TCGA-XE-AAOL    TCGA-XY-A89B    TCGA-XY-A8S2    TCGA-XY-A8S3 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-XY-A9T9    TCGA-YU-A90P    TCGA-YU-A90Q    TCGA-YU-A90S    TCGA-YU-A90W 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-YU-A90Y    TCGA-YU-A912    TCGA-YU-A94D    TCGA-YU-A94I    TCGA-YU-AA4L 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-YU-AA61    TCGA-ZM-AA05    TCGA-ZM-AA06    TCGA-ZM-AA0B    TCGA-ZM-AA0D 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-ZM-AA0E    TCGA-ZM-AA0F    TCGA-ZM-AA0H    TCGA-ZM-AA0N 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
               vv
clus            T1 T2 T3
  MFF MUTATED    3  0  0
  MFF WILD-TYPE 70 50  6
D43V4, multiclass
    clus
vv   MFF MUTATED MFF WILD-TYPE
  T1           3            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
  MFF MUTATED    2     0
  MFF WILD-TYPE 43    12
D43V5, multiclass
[1] "Remove cluster labels:" "MFF MUTATED"           
clus
  MFF MUTATED MFF WILD-TYPE 
            2            55 
   TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4    TCGA-2G-AAF6 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFI    TCGA-2G-AAFJ 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAFY    TCGA-2G-AAG0    TCGA-2G-AAG5    TCGA-2G-AAG6    TCGA-2G-AAG7 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAG8    TCGA-2G-AAG9    TCGA-2G-AAGA    TCGA-2G-AAGC    TCGA-2G-AAGE 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGF    TCGA-2G-AAGG    TCGA-2G-AAGI    TCGA-2G-AAGJ    TCGA-2G-AAGK 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGM    TCGA-2G-AAGN    TCGA-2G-AAGO    TCGA-2G-AAGP    TCGA-2G-AAGS 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAGW    TCGA-2G-AAGX    TCGA-2G-AAGY    TCGA-2G-AAGZ    TCGA-2G-AAH2 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAHG    TCGA-2G-AAHL    TCGA-2G-AAHN    TCGA-2G-AAHP    TCGA-2G-AAHT 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-2G-AAKG    TCGA-2G-AAL5    TCGA-2G-AAL7    TCGA-4K-AA1G    TCGA-4K-AA1H 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
   TCGA-4K-AA1I    TCGA-4K-AAAL    TCGA-SO-A8JP    TCGA-VF-A8AB    TCGA-X3-A8G4 
"MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" "MFF WILD-TYPE" 
D43V6, binary
               cls
clus              0   1
  MFF MUTATED     2   0
  MFF WILD-TYPE 110   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  MFF MUTATED      2    0
  MFF WILD-TYPE  110    4
   clus
vv  MFF MUTATED MFF WILD-TYPE
  0           2           110
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MFF MUTATED       0                         0     3
  MFF WILD-TYPE     4                         6   112
D43V7, multiclass
                           clus
vv                          MFF MUTATED MFF WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D43V8, binary
               cls
clus              0   1
  MFF MUTATED     0   3
  MFF WILD-TYPE  11 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  MFF MUTATED      0    3
  MFF WILD-TYPE   11  106
                        clus
vv                       MFF MUTATED MFF WILD-TYPE
  HISPANIC OR LATINO               0            11
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(44) Variable = PABPC3 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  PABPC3 MUTATED     3   0
  PABPC3 WILD-TYPE 123   4
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               3              127 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
               0                4 
$`PABPC3 MUTATED`
TCGA-2G-AAGX TCGA-4K-AA1I TCGA-4K-AAAL 
      170.33         0.10         4.83 

$`PABPC3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGY TCGA-2G-AAGZ 
       59.28       124.57       128.94        61.45        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  PABPC3 MUTATED PABPC3 WILD-TYPE 
            0.10             0.13 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
          170.33           229.22 
  PABPC3 MUTATED PABPC3 WILD-TYPE 
            4.83            38.30 
[1] "0.1 - 170.3 (4.8)"  "0.1 - 229.2 (38.3)"
[1] "hr="     "9100000"
D44V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PABPC3 MUTATED         0        2        0        0         0         0
  PABPC3 WILD-TYPE      19       22       11        5         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
                  vv
clus               STAGE IS
  PABPC3 MUTATED          1
  PABPC3 WILD-TYPE       45
D44V3, multiclass
            clus
vv           PABPC3 MUTATED PABPC3 WILD-TYPE
  STAGE I                 0               19
  STAGE IA                2               22
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 71 49  6
D44V4, multiclass
    clus
vv   PABPC3 MUTATED PABPC3 WILD-TYPE
  T1              2               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
  PABPC3 MUTATED    3     0
  PABPC3 WILD-TYPE 42    12
D44V5, multiclass
       clus
vv      PABPC3 MUTATED PABPC3 WILD-TYPE
  N0                 3               42
  N1+N2              0               12
[1] 2 2
[1] FALSE
D44V6, binary
                  cls
clus                 0   1
  PABPC3 MUTATED     3   0
  PABPC3 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      3    0
  PABPC3 WILD-TYPE  109    4
   clus
vv  PABPC3 MUTATED PABPC3 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC3 MUTATED       0                         0     3
  PABPC3 WILD-TYPE     4                         6   112
D44V7, multiclass
                           clus
vv                          PABPC3 MUTATED PABPC3 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D44V8, binary
                  cls
clus                 0   1
  PABPC3 MUTATED     0   3
  PABPC3 WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC3 MUTATED      0    3
  PABPC3 WILD-TYPE   11  106
                        clus
vv                       PABPC3 MUTATED PABPC3 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(45) Variable = CUX1 MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  CUX1 MUTATED     5   0
  CUX1 WILD-TYPE 121   4
  CUX1 MUTATED CUX1 WILD-TYPE 
             5            125 
  CUX1 MUTATED CUX1 WILD-TYPE 
             0              4 
$`CUX1 MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-VF-A8A8 TCGA-VF-A8AC 
       59.70        14.56        40.70        37.18        35.61 

$`CUX1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       36.99        14.14        17.16         9.57        14.86        16.50 
TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 
       36.13        36.89        40.01        52.37        71.24        72.20 
TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       61.71        63.22        63.32        68.22        72.85        68.38 
TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM 
       79.76        67.96        92.09        75.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        18.15         9.14        13.58         1.38        16.31 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB 
        9.63        10.26        17.23         3.52        37.68        24.99 
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         3.65         5.06 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 
        0.16         0.82        28.14         6.87        18.38        40.01 
TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 
       34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90        57.90 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D 
       54.35        31.92        21.96         0.56         5.29        58.88 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B 
        7.96        40.96         8.15        37.02        39.35        27.55 
TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       17.39        16.41        11.34        46.88        10.85 

  CUX1 MUTATED CUX1 WILD-TYPE 
         14.56           0.10 
  CUX1 MUTATED CUX1 WILD-TYPE 
         59.70         229.22 
  CUX1 MUTATED CUX1 WILD-TYPE 
         37.18          38.30 
[1] "14.6 - 59.7 (37.2)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.6e+07"
D45V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUX1 MUTATED         2        2        0        0         0         0
  CUX1 WILD-TYPE      17       22       11        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  CUX1 MUTATED           0         0          0          0          0        1
  CUX1 WILD-TYPE         1         2          1          6          5       45
D45V3, multiclass
            clus
vv           CUX1 MUTATED CUX1 WILD-TYPE
  STAGE I               2             17
  STAGE IA              2             22
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              1             45
[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 68 50  6
D45V4, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  T1            5             68
  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
D45V5, multiclass
       clus
vv      CUX1 MUTATED CUX1 WILD-TYPE
  N0               4             41
  N1+N2            0             12
[1] 2 2
[1] FALSE
D45V6, binary
                cls
clus               0   1
  CUX1 MUTATED     5   0
  CUX1 WILD-TYPE 107   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      5    0
  CUX1 WILD-TYPE  107    4
   clus
vv  CUX1 MUTATED CUX1 WILD-TYPE
  0            5            107
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUX1 MUTATED       1                         0     4
  CUX1 WILD-TYPE     3                         6   111
D45V7, multiclass
                           clus
vv                          CUX1 MUTATED CUX1 WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D45V8, binary
                cls
clus               0   1
  CUX1 MUTATED     0   5
  CUX1 WILD-TYPE  11 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED      0    5
  CUX1 WILD-TYPE   11  104
                        clus
vv                       CUX1 MUTATED CUX1 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(46) Variable = PCMTD1 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2                0   1
  PCMTD1 MUTATED     5   0
  PCMTD1 WILD-TYPE 121   4
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               5              125 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               0                4 
$`PCMTD1 MUTATED`
TCGA-2G-AAF4 TCGA-2G-AAFH TCGA-2G-AAGJ TCGA-2G-AAHP TCGA-ZM-AA0E 
       59.70        36.99        75.09       176.15        16.41 

$`PCMTD1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       20.32        30.35        38.30       102.35       122.40       191.31 
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       14.14        14.56        17.16         9.57        14.86        16.50 
TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAG5 
       40.70        36.13        36.89        40.01        52.37        71.24 
TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA TCGA-2G-AAGC 
       72.20        61.71        63.22        63.32        68.22        72.85 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       68.38        79.76        67.96        92.09       108.16        59.64 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
      106.39       115.00       120.62        59.28       124.57       128.94 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 
       61.45       170.33        80.94        60.16        60.26        59.84 
TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.90       125.69        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
       59.80        91.43         6.08       122.50       212.65       161.72 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 
       95.67       229.22       184.41       131.21        70.59         2.73 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW 
        0.13         3.52         7.00         0.10         4.83        20.68 
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         3.52        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         3.65 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 
        5.06         0.16         0.82        28.14         6.87        18.38 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        11.34        46.88        10.85 

  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           16.41             0.10 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
          176.15           229.22 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           59.70            37.68 
[1] "16.4 - 176.2 (59.7)" "0.1 - 229.2 (37.7)" 
[1] "hr="     "2.6e+07"
D46V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCMTD1 MUTATED         1        2        0        0         0         1
  PCMTD1 WILD-TYPE      18       22       11        5         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
                  vv
clus               STAGE IS
  PCMTD1 MUTATED          1
  PCMTD1 WILD-TYPE       45
D46V3, multiclass
            clus
vv           PCMTD1 MUTATED PCMTD1 WILD-TYPE
  STAGE I                 1               18
  STAGE IA                2               22
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 69 49  6
D46V4, multiclass
    clus
vv   PCMTD1 MUTATED PCMTD1 WILD-TYPE
  T1              4               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
  PCMTD1 MUTATED    3     1
  PCMTD1 WILD-TYPE 42    11
D46V5, multiclass
       clus
vv      PCMTD1 MUTATED PCMTD1 WILD-TYPE
  N0                 3               42
  N1+N2              1               11
[1] 2 2
[1] FALSE
D46V6, binary
                  cls
clus                 0   1
  PCMTD1 MUTATED     5   0
  PCMTD1 WILD-TYPE 107   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      5    0
  PCMTD1 WILD-TYPE  107    4
   clus
vv  PCMTD1 MUTATED PCMTD1 WILD-TYPE
  0              5              107
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCMTD1 MUTATED       0                         1     4
  PCMTD1 WILD-TYPE     4                         5   111
D46V7, multiclass
                           clus
vv                          PCMTD1 MUTATED PCMTD1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                  4              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"
D46V8, binary
                  cls
clus                 0   1
  PCMTD1 MUTATED     0   5
  PCMTD1 WILD-TYPE  11 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      0    5
  PCMTD1 WILD-TYPE   11  104
                        clus
vv                       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              5              104
[1] 2 2
[1] FALSE

Clustering(47) Variable = EZH2 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED     4   0
  EZH2 WILD-TYPE 122   4
  EZH2 MUTATED EZH2 WILD-TYPE 
             4            126 
  EZH2 MUTATED EZH2 WILD-TYPE 
             0              4 
$`EZH2 MUTATED`
TCGA-2G-AAFN TCGA-VF-A8AD TCGA-WZ-A7V5 TCGA-XE-A8H4 
       14.86        33.07         0.16        18.38 

$`EZH2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
TCGA-VF-A8A8 TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 
       37.18        37.68        24.99        35.61        23.90        41.52 
TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.26         3.65         5.06         0.82        28.14         6.87 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  EZH2 MUTATED EZH2 WILD-TYPE 
          0.16           0.10 
  EZH2 MUTATED EZH2 WILD-TYPE 
         33.07         229.22 
  EZH2 MUTATED EZH2 WILD-TYPE 
         16.62          39.68 
[1] "0.2 - 33.1 (16.6)"  "0.1 - 229.2 (39.7)"
[1] "hr="     "9200000"
D47V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EZH2 MUTATED         1        1        1        0         0         0
  EZH2 WILD-TYPE      18       23       10        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  EZH2 MUTATED           0         0          0          1          0        0
  EZH2 WILD-TYPE         1         2          1          5          5       46
D47V3, multiclass
            clus
vv           EZH2 MUTATED EZH2 WILD-TYPE
  STAGE I               1             18
  STAGE IA              1             23
  STAGE IB              1             10
  STAGE II              0              5
  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
  STAGE IS              0             46
[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 73 47  6
D47V4, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  T1            0             73
  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
D47V5, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             1             56 
    TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1     TCGA-2G-AAF4 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG     TCGA-2G-AAFH 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL     TCGA-2G-AAFM 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY     TCGA-2G-AAG0 
"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" 
D47V6, binary
                cls
clus               0   1
  EZH2 MUTATED     3   0
  EZH2 WILD-TYPE 109   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      3    0
  EZH2 WILD-TYPE  109    4
   clus
vv  EZH2 MUTATED EZH2 WILD-TYPE
  0            3            109
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED       0                         0     4
  EZH2 WILD-TYPE     4                         6   111
D47V7, multiclass
                           clus
vv                          EZH2 MUTATED EZH2 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                4            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"
D47V8, binary
                cls
clus               0   1
  EZH2 MUTATED     0   4
  EZH2 WILD-TYPE  11 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      0    4
  EZH2 WILD-TYPE   11  105
                        clus
vv                       EZH2 MUTATED EZH2 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            4            105
[1] 2 2
[1] FALSE

Clustering(48) Variable = HTT MUTATION ANALYSIS
D48V1, survival
               sevent
clus2             0   1
  HTT MUTATED     3   0
  HTT WILD-TYPE 123   4
  HTT MUTATED HTT WILD-TYPE 
            3           127 
  HTT MUTATED HTT WILD-TYPE 
            0             4 
$`HTT MUTATED`
TCGA-2G-AAFI TCGA-SN-A6IS TCGA-ZM-AA0H 
       14.14        16.31        46.88 

$`HTT WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
      191.31        36.99        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        18.15         9.14        13.58 
TCGA-SB-A76C TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 
        1.38         9.63        10.26        17.23         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F 
       37.02        39.35        27.55        17.39        16.41        11.34 
TCGA-ZM-AA0N 
       10.85 

  HTT MUTATED HTT WILD-TYPE 
        14.14          0.10 
  HTT MUTATED HTT WILD-TYPE 
        46.88        229.22 
  HTT MUTATED HTT WILD-TYPE 
        16.31         38.30 
[1] "14.1 - 46.9 (16.3)" "0.1 - 229.2 (38.3)"
[1] "hr="     "9100000"
D48V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTT MUTATED         0        0        1        0         0         0
  HTT WILD-TYPE      19       24       10        5         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  HTT MUTATED           0         0          0          0          0        2
  HTT WILD-TYPE         1         2          1          6          5       44
D48V3, multiclass
            clus
vv           HTT MUTATED HTT WILD-TYPE
  STAGE I              0            19
  STAGE IA             0            24
  STAGE IB             1            10
  STAGE II             0             5
  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
  STAGE IS             2            44
[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 72 49  5
D48V4, multiclass
    clus
vv   HTT MUTATED HTT WILD-TYPE
  T1           1            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
  HTT MUTATED    1     0
  HTT WILD-TYPE 44    12
D48V5, multiclass
[1] "Remove cluster labels:" "HTT MUTATED"           
clus
  HTT MUTATED HTT WILD-TYPE 
            1            56 
   TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4    TCGA-2G-AAF6 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFJ    TCGA-2G-AAFL 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV    TCGA-2G-AAFY 
"HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" "HTT WILD-TYPE" 
   TCGA-2G-AAG0    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" 
D48V6, binary
               cls
clus              0   1
  HTT MUTATED     3   0
  HTT WILD-TYPE 109   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  HTT MUTATED      3    0
  HTT WILD-TYPE  109    4
   clus
vv  HTT MUTATED HTT WILD-TYPE
  0           3           109
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTT MUTATED       0                         0     3
  HTT WILD-TYPE     4                         6   112
D48V7, multiclass
                           clus
vv                          HTT MUTATED HTT WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D48V8, binary
               cls
clus              0   1
  HTT MUTATED     1   2
  HTT WILD-TYPE  10 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  HTT MUTATED      1    2
  HTT WILD-TYPE   10  107
                        clus
vv                       HTT MUTATED HTT WILD-TYPE
  HISPANIC OR LATINO               1            10
  NOT HISPANIC OR LATINO           2           107
[1] 2 2
[1] FALSE

Clustering(49) Variable = AHDC1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  AHDC1 MUTATED     3   0
  AHDC1 WILD-TYPE 123   4
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              3             127 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              0               4 
$`AHDC1 MUTATED`
TCGA-2G-AAG5 TCGA-2G-AAGM TCGA-2G-AAH4 
       71.24        59.64       125.69 

$`AHDC1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       52.37        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
      108.16       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG 
       59.84        59.90        61.84        98.53        59.74        59.80 
TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG 
       59.80        91.43       176.15         6.08       122.50       212.65 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP 
      161.72        95.67       229.22       184.41       131.21        70.59 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL 
        2.73         0.13         3.52         7.00         0.10         4.83 
TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS 
       20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  AHDC1 MUTATED AHDC1 WILD-TYPE 
          59.64            0.10 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
         125.69          229.22 
  AHDC1 MUTATED AHDC1 WILD-TYPE 
          71.24           37.18 
[1] "59.6 - 125.7 (71.2)" "0.1 - 229.2 (37.2)" 
[1] "hr="     "2.5e+07"
D49V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AHDC1 MUTATED         0        0        0        1         0         0
  AHDC1 WILD-TYPE      19       24       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  AHDC1 MUTATED           0         0          0          0          0        2
  AHDC1 WILD-TYPE         1         2          1          6          5       44
D49V3, multiclass
            clus
vv           AHDC1 MUTATED AHDC1 WILD-TYPE
  STAGE I                0              19
  STAGE IA               0              24
  STAGE IB               0              11
  STAGE II               1               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
  STAGE IS               2              44
[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 71 49  6
D49V4, multiclass
    clus
vv   AHDC1 MUTATED AHDC1 WILD-TYPE
  T1             2              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
  AHDC1 MUTATED    2     0
  AHDC1 WILD-TYPE 43    12
D49V5, multiclass
[1] "Remove cluster labels:" "AHDC1 MUTATED"         
clus
  AHDC1 MUTATED AHDC1 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" "AHDC1 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D49V6, binary
                 cls
clus                0   1
  AHDC1 MUTATED     3   0
  AHDC1 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      3    0
  AHDC1 WILD-TYPE  109    4
   clus
vv  AHDC1 MUTATED AHDC1 WILD-TYPE
  0             3             109
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AHDC1 MUTATED       0                         0     3
  AHDC1 WILD-TYPE     4                         6   112
D49V7, multiclass
                           clus
vv                          AHDC1 MUTATED AHDC1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 3             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"
D49V8, binary
                 cls
clus                0   1
  AHDC1 MUTATED     0   3
  AHDC1 WILD-TYPE  11 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AHDC1 MUTATED      0    3
  AHDC1 WILD-TYPE   11  106
                        clus
vv                       AHDC1 MUTATED AHDC1 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(50) Variable = RFC3 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  RFC3 MUTATED     3   0
  RFC3 WILD-TYPE 123   4
  RFC3 MUTATED RFC3 WILD-TYPE 
             3            127 
  RFC3 MUTATED RFC3 WILD-TYPE 
             0              4 
$`RFC3 MUTATED`
TCGA-2G-AAFY TCGA-2G-AAGC TCGA-SN-A6IS 
       36.13        72.85        16.31 

$`RFC3 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       14.86        16.50        40.70        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ TCGA-2G-AAGK 
       68.38        79.76        67.96        92.09        75.09       108.16 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS TCGA-2G-AAGT 
       59.64       106.39       115.00       120.62        59.28       124.57 
TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      128.94        61.45       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        18.15         9.14        13.58         1.38 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-SO-A8JP TCGA-VF-A8A8 TCGA-VF-A8AA 
        9.63        10.26        17.23         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  RFC3 MUTATED RFC3 WILD-TYPE 
         16.31           0.10 
  RFC3 MUTATED RFC3 WILD-TYPE 
         72.85         229.22 
  RFC3 MUTATED RFC3 WILD-TYPE 
         36.13          38.30 
[1] "16.3 - 72.8 (36.1)" "0.1 - 229.2 (38.3)"
[1] "hr="     "9200000"
D50V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RFC3 MUTATED         0        0        0        0         1         0
  RFC3 WILD-TYPE      19       24       11        5         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RFC3 MUTATED           0         0          0          0          0        2
  RFC3 WILD-TYPE         1         2          1          6          5       44
D50V3, multiclass
            clus
vv           RFC3 MUTATED RFC3 WILD-TYPE
  STAGE I               0             19
  STAGE IA              0             24
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              2             44
[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
  RFC3 MUTATED    2  1  0
  RFC3 WILD-TYPE 71 49  6
D50V4, multiclass
    clus
vv   RFC3 MUTATED RFC3 WILD-TYPE
  T1            2             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
  RFC3 MUTATED    1     1
  RFC3 WILD-TYPE 44    11
D50V5, multiclass
[1] "Remove cluster labels:" "RFC3 MUTATED"          
clus
  RFC3 MUTATED RFC3 WILD-TYPE 
             2             55 
    TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1     TCGA-2G-AAF4 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG     TCGA-2G-AAFH 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL     TCGA-2G-AAFM 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAFN     TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAG0 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAG5     TCGA-2G-AAG6     TCGA-2G-AAG7     TCGA-2G-AAG8 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAG9     TCGA-2G-AAGA     TCGA-2G-AAGE     TCGA-2G-AAGF 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAGG     TCGA-2G-AAGI     TCGA-2G-AAGJ     TCGA-2G-AAGK 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAGM     TCGA-2G-AAGN     TCGA-2G-AAGO     TCGA-2G-AAGP 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAGS     TCGA-2G-AAGW     TCGA-2G-AAGX     TCGA-2G-AAGY 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAGZ     TCGA-2G-AAH2     TCGA-2G-AAHG     TCGA-2G-AAHL 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAHN     TCGA-2G-AAHP     TCGA-2G-AAHT     TCGA-2G-AAKG 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-2G-AAL5     TCGA-2G-AAL7     TCGA-4K-AA1G     TCGA-4K-AA1H 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-4K-AA1I     TCGA-4K-AAAL     TCGA-SO-A8JP     TCGA-VF-A8A8 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
    TCGA-VF-A8AA     TCGA-VF-A8AB     TCGA-X3-A8G4 
"RFC3 WILD-TYPE" "RFC3 WILD-TYPE" "RFC3 WILD-TYPE" 
D50V6, binary
                cls
clus               0   1
  RFC3 MUTATED     3   0
  RFC3 WILD-TYPE 109   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFC3 MUTATED      3    0
  RFC3 WILD-TYPE  109    4
   clus
vv  RFC3 MUTATED RFC3 WILD-TYPE
  0            3            109
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RFC3 MUTATED       0                         0     3
  RFC3 WILD-TYPE     4                         6   112
D50V7, multiclass
                           clus
vv                          RFC3 MUTATED RFC3 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            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"
D50V8, binary
                cls
clus               0   1
  RFC3 MUTATED     1   2
  RFC3 WILD-TYPE  10 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFC3 MUTATED      1    2
  RFC3 WILD-TYPE   10  107
                        clus
vv                       RFC3 MUTATED RFC3 WILD-TYPE
  HISPANIC OR LATINO                1             10
  NOT HISPANIC OR LATINO            2            107
[1] 2 2
[1] FALSE

Clustering(51) Variable = CHD4 MUTATION ANALYSIS
D51V1, survival
                sevent
clus2              0   1
  CHD4 MUTATED     2   1
  CHD4 WILD-TYPE 124   3
  CHD4 MUTATED CHD4 WILD-TYPE 
             3            127 
  CHD4 MUTATED CHD4 WILD-TYPE 
             1              3 
$`CHD4 MUTATED`
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-YU-A90Y 
       41.69         0.43         0.56 

$`CHD4 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.16 
TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI 
        0.82        28.14         6.87        18.38        40.01        34.22 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        53.03        93.93        12.07         7.89 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOJ TCGA-XY-A89B TCGA-XY-A8S2 
       16.87         8.88        67.66        50.96         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  CHD4 MUTATED CHD4 WILD-TYPE 
          0.43           0.10 
  CHD4 MUTATED CHD4 WILD-TYPE 
         41.69         229.22 
  CHD4 MUTATED CHD4 WILD-TYPE 
          0.56          38.30 
[1] "0.4 - 41.7 (0.6)"   "0.1 - 229.2 (38.3)"
[1] "hr=" "38" 
D51V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHD4 MUTATED         1        1        0        0         0         0
  CHD4 WILD-TYPE      18       23       11        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  CHD4 MUTATED           0         0          0          0          1        0
  CHD4 WILD-TYPE         1         2          1          6          4       46
D51V3, multiclass
            clus
vv           CHD4 MUTATED CHD4 WILD-TYPE
  STAGE I               1             18
  STAGE IA              1             23
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              0             46
[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
  CHD4 MUTATED    2  0  1
  CHD4 WILD-TYPE 71 50  5
D51V4, multiclass
    clus
vv   CHD4 MUTATED CHD4 WILD-TYPE
  T1            2             71
  T2            0             50
  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
  CHD4 MUTATED    0     0
  CHD4 WILD-TYPE 45    12
D51V5, multiclass
D51V6, binary
                cls
clus               0   1
  CHD4 MUTATED     2   0
  CHD4 WILD-TYPE 110   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED      2    0
  CHD4 WILD-TYPE  110    4
   clus
vv  CHD4 MUTATED CHD4 WILD-TYPE
  0            2            110
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHD4 MUTATED       1                         2     0
  CHD4 WILD-TYPE     3                         4   115
D51V7, multiclass
                           clus
vv                          CHD4 MUTATED CHD4 WILD-TYPE
  ASIAN                                1              3
  BLACK OR AFRICAN AMERICAN            2              4
  WHITE                                0            115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                cls
clus               0   1
  CHD4 MUTATED     0   2
  CHD4 WILD-TYPE  11 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD4 MUTATED      0    2
  CHD4 WILD-TYPE   11  107
                        clus
vv                       CHD4 MUTATED CHD4 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            2            107
[1] 2 2
[1] FALSE

Clustering(52) Variable = RUNX2 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2               0   1
  RUNX2 MUTATED     4   0
  RUNX2 WILD-TYPE 122   4
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              4             126 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              0               4 
$`RUNX2 MUTATED`
TCGA-2G-AAG3 TCGA-2G-AAGW TCGA-SB-A6J6 TCGA-YU-A912 
       52.37        61.45        13.58         5.29 

$`RUNX2 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ TCGA-2G-AAH0 
      124.57       128.94       170.33        80.94        60.16        60.26 
TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
       59.84        59.90       125.69        61.84        98.53        59.74 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2G-AAKD 
       59.80        59.80        91.43       176.15         6.08       122.50 
TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      212.65       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C TCGA-SN-A6IS 
        4.83        20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
           5.29            0.10 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          61.45          229.22 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
         32.975          37.990 
[1] "5.3 - 61.5 (33.0)"  "0.1 - 229.2 (38.0)"
[1] "hr="     "2.5e+07"
D52V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUNX2 MUTATED         0        1        0        0         0         0
  RUNX2 WILD-TYPE      19       23       11        5         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  RUNX2 MUTATED           0         0          0          0          1        2
  RUNX2 WILD-TYPE         1         2          1          6          4       44
D52V3, multiclass
            clus
vv           RUNX2 MUTATED RUNX2 WILD-TYPE
  STAGE I                0              19
  STAGE IA               1              23
  STAGE IB               0              11
  STAGE II               0               5
  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
  STAGE IS               2              44
[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 70 49  6
D52V4, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  T1             3              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
  RUNX2 MUTATED    1     0
  RUNX2 WILD-TYPE 44    12
D52V5, multiclass
[1] "Remove cluster labels:" "RUNX2 MUTATED"         
clus
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              1              56 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" "RUNX2 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D52V6, binary
                 cls
clus                0   1
  RUNX2 MUTATED     3   0
  RUNX2 WILD-TYPE 109   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      3    0
  RUNX2 WILD-TYPE  109    4
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             3             109
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX2 MUTATED       0                         1     3
  RUNX2 WILD-TYPE     4                         5   112
D52V7, multiclass
                           clus
vv                          RUNX2 MUTATED RUNX2 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 3             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"
D52V8, binary
                 cls
clus                0   1
  RUNX2 MUTATED     0   3
  RUNX2 WILD-TYPE  11 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      0    3
  RUNX2 WILD-TYPE   11  106
                        clus
vv                       RUNX2 MUTATED RUNX2 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             3             106
[1] 2 2
[1] FALSE

Clustering(53) Variable = SP4 MUTATION ANALYSIS
D53V1, survival
               sevent
clus2             0   1
  SP4 MUTATED     3   0
  SP4 WILD-TYPE 123   4
  SP4 MUTATED SP4 WILD-TYPE 
            3           127 
  SP4 MUTATED SP4 WILD-TYPE 
            0             4 
$`SP4 MUTATED`
TCGA-2G-AAGA TCGA-2G-AAKG TCGA-XY-A8S2 
       68.22       212.65        12.92 

$`SP4 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 
      122.50       161.72        95.67       229.22       184.41       131.21 
TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       70.59         2.73         0.13         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR 
        6.87        18.38        40.01        34.22        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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-A8S3 
       67.66        41.69        50.96         0.43         8.32        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  SP4 MUTATED SP4 WILD-TYPE 
        12.92          0.10 
  SP4 MUTATED SP4 WILD-TYPE 
       212.65        229.22 
  SP4 MUTATED SP4 WILD-TYPE 
        68.22         37.68 
[1] "12.9 - 212.7 (68.2)" "0.1 - 229.2 (37.7)" 
[1] "hr="     "9200000"
D53V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP4 MUTATED         2        0        0        0         1         0
  SP4 WILD-TYPE      17       24       11        5         4         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  SP4 MUTATED           0         0          0          0          0        0
  SP4 WILD-TYPE         1         2          1          6          5       46
D53V3, multiclass
            clus
vv           SP4 MUTATED SP4 WILD-TYPE
  STAGE I              2            17
  STAGE IA             0            24
  STAGE IB             0            11
  STAGE II             0             5
  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
  STAGE IS             0            46
[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 71 49  6
D53V4, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  T1           2            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
  SP4 MUTATED    1     1
  SP4 WILD-TYPE 44    11
D53V5, multiclass
[1] "Remove cluster labels:" "SP4 MUTATED"           
clus
  SP4 MUTATED SP4 WILD-TYPE 
            2            55 
   TCGA-2G-AAEW    TCGA-2G-AAEX    TCGA-2G-AAF1    TCGA-2G-AAF4    TCGA-2G-AAF6 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAF8    TCGA-2G-AAFG    TCGA-2G-AAFH    TCGA-2G-AAFI    TCGA-2G-AAFJ 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFL    TCGA-2G-AAFM    TCGA-2G-AAFN    TCGA-2G-AAFO    TCGA-2G-AAFV 
"SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" "SP4 WILD-TYPE" 
   TCGA-2G-AAFY    TCGA-2G-AAG0    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" 
D53V6, binary
               cls
clus              0   1
  SP4 MUTATED     3   0
  SP4 WILD-TYPE 109   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      3    0
  SP4 WILD-TYPE  109    4
   clus
vv  SP4 MUTATED SP4 WILD-TYPE
  0           3           109
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP4 MUTATED       0                         0     3
  SP4 WILD-TYPE     4                         6   112
D53V7, multiclass
                           clus
vv                          SP4 MUTATED SP4 WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D53V8, binary
               cls
clus              0   1
  SP4 MUTATED     0   3
  SP4 WILD-TYPE  11 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      0    3
  SP4 WILD-TYPE   11  106
                        clus
vv                       SP4 MUTATED SP4 WILD-TYPE
  HISPANIC OR LATINO               0            11
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(54) Variable = DIAPH1 MUTATION ANALYSIS
D54V1, survival
                  sevent
clus2                0   1
  DIAPH1 MUTATED     3   0
  DIAPH1 WILD-TYPE 123   4
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               3              127 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               0                4 
$`DIAPH1 MUTATED`
TCGA-WZ-A8D5 TCGA-XE-AANI TCGA-ZM-AA0E 
        0.82        34.22        16.41 

$`DIAPH1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 
       60.16        60.26        59.84        59.90       125.69        61.84 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP 
       98.53        59.74        59.80        59.80        91.43       176.15 
TCGA-2G-AAHT TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM 
        6.08       122.50       212.65       161.72        95.67       229.22 
TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      184.41       131.21        70.59         2.73         0.13         3.52 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
        7.00         0.10         4.83        20.68        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 
        3.52        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         3.65         5.06         0.16 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR 
       28.14         6.87        18.38        40.01        65.98         0.46 
TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC 
       53.03        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         8.32        12.92 
TCGA-XY-A8S3 TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
       20.12         6.90        57.90        54.35        31.92        21.96 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
        0.56         5.29        58.88         7.96        40.96         8.15 
TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       37.02        39.35        27.55        17.39        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
            0.82             0.10 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
           34.22           229.22 
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
           16.41            39.35 
[1] "0.8 - 34.2 (16.4)"  "0.1 - 229.2 (39.4)"
[1] "hr="     "9100000"
D54V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DIAPH1 MUTATED         0        1        0        0         0         0
  DIAPH1 WILD-TYPE      19       23       11        5         5         1
                  vv
clus               STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DIAPH1 MUTATED           0         0          0          0          0
  DIAPH1 WILD-TYPE         1         2          1          6          5
                  vv
clus               STAGE IS
  DIAPH1 MUTATED          1
  DIAPH1 WILD-TYPE       45
D54V3, multiclass
[1] "Remove cluster labels:" "DIAPH1 MUTATED"        
clus
  DIAPH1 MUTATED DIAPH1 WILD-TYPE 
               2              124 
      TCGA-2G-AAEW       TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAF6       TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAFI       TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAFN       TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAFZ       TCGA-2G-AAG0       TCGA-2G-AAG3       TCGA-2G-AAG5 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAG6       TCGA-2G-AAG7       TCGA-2G-AAG8       TCGA-2G-AAG9 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAGA       TCGA-2G-AAGC       TCGA-2G-AAGE       TCGA-2G-AAGF 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAGG       TCGA-2G-AAGI       TCGA-2G-AAGJ       TCGA-2G-AAGK 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAGM       TCGA-2G-AAGN       TCGA-2G-AAGO       TCGA-2G-AAGP 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAGS       TCGA-2G-AAGT       TCGA-2G-AAGV       TCGA-2G-AAGW 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAGX       TCGA-2G-AAGY       TCGA-2G-AAGZ       TCGA-2G-AAH0 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAH2       TCGA-2G-AAH3       TCGA-2G-AAH4       TCGA-2G-AAH8 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAHA       TCGA-2G-AAHC       TCGA-2G-AAHG       TCGA-2G-AAHL 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAHN       TCGA-2G-AAHP       TCGA-2G-AAHT       TCGA-2G-AAKD 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAKG       TCGA-2G-AAKH       TCGA-2G-AAKL       TCGA-2G-AAKM 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2G-AAL5       TCGA-2G-AAL7       TCGA-2G-AALP       TCGA-2X-A9D5 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-2X-A9D6       TCGA-4K-AA1G       TCGA-4K-AA1H       TCGA-4K-AA1I 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-4K-AAAL       TCGA-S6-A8JW       TCGA-S6-A8JX       TCGA-S6-A8JY 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-SB-A6J6       TCGA-SN-A6IS       TCGA-SN-A84W       TCGA-SN-A84X 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-SN-A84Y       TCGA-SO-A8JP       TCGA-VF-A8A8       TCGA-VF-A8AA 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-VF-A8AB       TCGA-VF-A8AC       TCGA-VF-A8AD       TCGA-VF-A8AE 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-WZ-A7V3       TCGA-WZ-A7V4       TCGA-WZ-A7V5       TCGA-X3-A8G4 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-XE-A8H1       TCGA-XE-A8H4       TCGA-XE-A8H5       TCGA-XE-AANJ 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-XE-AANR       TCGA-XE-AANV       TCGA-XE-AAO3       TCGA-XE-AAO4 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-XE-AAO6       TCGA-XE-AAOB       TCGA-XE-AAOC       TCGA-XE-AAOD 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-XE-AAOF       TCGA-XE-AAOJ       TCGA-XE-AAOL       TCGA-XY-A89B 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-XY-A8S2       TCGA-XY-A8S3       TCGA-XY-A9T9       TCGA-YU-A90P 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-YU-A90Q       TCGA-YU-A90S       TCGA-YU-A90W       TCGA-YU-A90Y 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-YU-A912       TCGA-YU-A94D       TCGA-YU-A94I       TCGA-YU-AA4L 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-YU-AA61       TCGA-ZM-AA05       TCGA-ZM-AA06       TCGA-ZM-AA0B 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
      TCGA-ZM-AA0D       TCGA-ZM-AA0F       TCGA-ZM-AA0H       TCGA-ZM-AA0N 
"DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" "DIAPH1 WILD-TYPE" 
                  vv
clus               T1 T2 T3
  DIAPH1 MUTATED    2  0  1
  DIAPH1 WILD-TYPE 71 50  5
D54V4, multiclass
    clus
vv   DIAPH1 MUTATED DIAPH1 WILD-TYPE
  T1              2               71
  T2              0               50
  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
  DIAPH1 MUTATED    0     0
  DIAPH1 WILD-TYPE 45    12
D54V5, multiclass
D54V6, binary
                  cls
clus                 0   1
  DIAPH1 MUTATED     3   0
  DIAPH1 WILD-TYPE 109   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH1 MUTATED      3    0
  DIAPH1 WILD-TYPE  109    4
   clus
vv  DIAPH1 MUTATED DIAPH1 WILD-TYPE
  0              3              109
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIAPH1 MUTATED       0                         0     3
  DIAPH1 WILD-TYPE     4                         6   112
D54V7, multiclass
                           clus
vv                          DIAPH1 MUTATED DIAPH1 WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D54V8, binary
                  cls
clus                 0   1
  DIAPH1 MUTATED     0   3
  DIAPH1 WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH1 MUTATED      0    3
  DIAPH1 WILD-TYPE   11  106
                        clus
vv                       DIAPH1 MUTATED DIAPH1 WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(55) Variable = PLEC MUTATION ANALYSIS
D55V1, survival
                sevent
clus2              0   1
  PLEC MUTATED     6   0
  PLEC WILD-TYPE 120   4
  PLEC MUTATED PLEC WILD-TYPE 
             6            124 
  PLEC MUTATED PLEC WILD-TYPE 
             0              4 
$`PLEC MUTATED`
TCGA-2G-AAFM TCGA-2X-A9D6 TCGA-XE-A8H4 TCGA-XE-AAOD TCGA-YU-A94I TCGA-ZM-AA05 
        9.57         0.13        18.38        67.66         7.96        37.02 

$`PLEC WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFN 
      191.31        36.99        14.14        14.56        17.16        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         2.73         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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         3.65         5.06         0.16         0.82        28.14 
TCGA-XE-A8H1 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
        6.87        40.01        34.22        65.98         0.46        53.03 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOF 
       93.93        12.07         7.89        16.87         8.88        41.69 
TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-XY-A9T9 
       50.96         0.43         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       58.88        40.96         8.15        39.35        27.55        17.39 
TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       16.41        11.34        46.88        10.85 

  PLEC MUTATED PLEC WILD-TYPE 
          0.13           0.10 
  PLEC MUTATED PLEC WILD-TYPE 
         67.66         229.22 
  PLEC MUTATED PLEC WILD-TYPE 
        13.975         39.680 
[1] "0.1 - 67.7 (14.0)"  "0.1 - 229.2 (39.7)"
[1] "hr="     "2.6e+07"
D55V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEC MUTATED         1        2        1        0         1         0
  PLEC WILD-TYPE      18       22       10        5         4         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  PLEC MUTATED           1         0          0          0          0        0
  PLEC WILD-TYPE         0         2          1          6          5       46
D55V3, multiclass
            clus
vv           PLEC MUTATED PLEC WILD-TYPE
  STAGE I               1             18
  STAGE IA              2             22
  STAGE IB              1             10
  STAGE II              0              5
  STAGE IIA             1              4
  STAGE IIB             0              1
  STAGE IIC             1              0
  STAGE III             0              2
  STAGE IIIA            0              1
  STAGE IIIB            0              6
  STAGE IIIC            0              5
  STAGE IS              0             46
[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
  PLEC MUTATED    2  3  0
  PLEC WILD-TYPE 71 47  6
D55V4, multiclass
    clus
vv   PLEC MUTATED PLEC WILD-TYPE
  T1            2             71
  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
  PLEC MUTATED    0     1
  PLEC WILD-TYPE 45    11
D55V5, multiclass
[1] "Remove cluster labels:" "PLEC MUTATED"          
clus
  PLEC MUTATED PLEC WILD-TYPE 
             1             56 
    TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1     TCGA-2G-AAF4 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG     TCGA-2G-AAFH 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL     TCGA-2G-AAFN 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY     TCGA-2G-AAG0 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAG5     TCGA-2G-AAG6     TCGA-2G-AAG7     TCGA-2G-AAG8 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAG9     TCGA-2G-AAGA     TCGA-2G-AAGC     TCGA-2G-AAGE 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAGF     TCGA-2G-AAGG     TCGA-2G-AAGI     TCGA-2G-AAGJ 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAGK     TCGA-2G-AAGM     TCGA-2G-AAGN     TCGA-2G-AAGO 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAGP     TCGA-2G-AAGS     TCGA-2G-AAGW     TCGA-2G-AAGX 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAGY     TCGA-2G-AAGZ     TCGA-2G-AAH2     TCGA-2G-AAHG 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAHL     TCGA-2G-AAHN     TCGA-2G-AAHP     TCGA-2G-AAHT 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-2G-AAKG     TCGA-2G-AAL5     TCGA-2G-AAL7     TCGA-4K-AA1G 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-4K-AA1H     TCGA-4K-AA1I     TCGA-4K-AAAL     TCGA-SO-A8JP 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
    TCGA-VF-A8A8     TCGA-VF-A8AA     TCGA-VF-A8AB     TCGA-X3-A8G4 
"PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" "PLEC WILD-TYPE" 
D55V6, binary
                cls
clus               0   1
  PLEC MUTATED     5   0
  PLEC WILD-TYPE 107   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      5    0
  PLEC WILD-TYPE  107    4
   clus
vv  PLEC MUTATED PLEC WILD-TYPE
  0            5            107
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEC MUTATED       0                         0     5
  PLEC WILD-TYPE     4                         6   110
D55V7, multiclass
                           clus
vv                          PLEC MUTATED PLEC WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                5            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"
D55V8, binary
                cls
clus               0   1
  PLEC MUTATED     0   5
  PLEC WILD-TYPE  11 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEC MUTATED      0    5
  PLEC WILD-TYPE   11  104
                        clus
vv                       PLEC MUTATED PLEC WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            5            104
[1] 2 2
[1] FALSE

Clustering(56) Variable = NHS MUTATION ANALYSIS
D56V1, survival
               sevent
clus2             0   1
  NHS MUTATED     3   0
  NHS WILD-TYPE 123   4
  NHS MUTATED NHS WILD-TYPE 
            3           127 
  NHS MUTATED NHS WILD-TYPE 
            0             4 
$`NHS MUTATED`
TCGA-2G-AAG9 TCGA-VF-A8A8 TCGA-VF-A8AA 
       63.32        37.18        37.68 

$`NHS WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA 
       52.37        71.24        72.20        61.71        63.22        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  NHS MUTATED NHS WILD-TYPE 
        37.18          0.10 
  NHS MUTATED NHS WILD-TYPE 
        63.32        229.22 
  NHS MUTATED NHS WILD-TYPE 
        37.68         38.30 
[1] "37.2 - 63.3 (37.7)" "0.1 - 229.2 (38.3)"
[1] "hr="     "2.5e+07"
D56V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NHS MUTATED         1        1        0        0         0         0
  NHS WILD-TYPE      18       23       11        5         5         1
               vv
clus            STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  NHS MUTATED           0         0          0          1          0        0
  NHS WILD-TYPE         1         2          1          5          5       46
D56V3, multiclass
            clus
vv           NHS MUTATED NHS WILD-TYPE
  STAGE I              1            18
  STAGE IA             1            23
  STAGE IB             0            11
  STAGE II             0             5
  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
  STAGE IS             0            46
[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
  NHS MUTATED    2  1  0
  NHS WILD-TYPE 71 49  6
D56V4, multiclass
    clus
vv   NHS MUTATED NHS WILD-TYPE
  T1           2            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
  NHS MUTATED    2     1
  NHS WILD-TYPE 43    11
D56V5, multiclass
       clus
vv      NHS MUTATED NHS WILD-TYPE
  N0              2            43
  N1+N2           1            11
[1] 2 2
[1] FALSE
D56V6, binary
               cls
clus              0   1
  NHS MUTATED     3   0
  NHS WILD-TYPE 109   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      3    0
  NHS WILD-TYPE  109    4
   clus
vv  NHS MUTATED NHS WILD-TYPE
  0           3           109
  1           0             4
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NHS MUTATED       0                         0     3
  NHS WILD-TYPE     4                         6   112
D56V7, multiclass
                           clus
vv                          NHS MUTATED NHS WILD-TYPE
  ASIAN                               0             4
  BLACK OR AFRICAN AMERICAN           0             6
  WHITE                               3           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"
D56V8, binary
               cls
clus              0   1
  NHS MUTATED     0   3
  NHS WILD-TYPE  11 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  NHS MUTATED      0    3
  NHS WILD-TYPE   11  106
                        clus
vv                       NHS MUTATED NHS WILD-TYPE
  HISPANIC OR LATINO               0            11
  NOT HISPANIC OR LATINO           3           106
[1] 2 2
[1] FALSE

Clustering(57) Variable = PIK3CD MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  PIK3CD MUTATED     2   1
  PIK3CD WILD-TYPE 124   3
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               3              127 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               1                3 
$`PIK3CD MUTATED`
TCGA-2G-AAEW TCGA-VF-A8AA TCGA-WZ-A7V4 
       20.32        37.68         5.06 

$`PIK3CD WILD-TYPE`
TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG 
       30.35        38.30        59.70       102.35       122.40       191.31 
TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN 
       36.99        14.14        14.56        17.16         9.57        14.86 
TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 TCGA-2G-AAG3 
       16.50        40.70        36.13        36.89        40.01        52.37 
TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 TCGA-2G-AAGA 
       71.24        72.20        61.71        63.22        63.32        68.22 
TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGJ 
       72.85        68.38        79.76        67.96        92.09        75.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 
        0.10         4.83        20.68        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         3.52 
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-A7V5 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       24.26         3.65         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  PIK3CD MUTATED PIK3CD WILD-TYPE 
            5.06             0.10 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
           37.68           229.22 
  PIK3CD MUTATED PIK3CD WILD-TYPE 
           20.32            39.35 
[1] "5.1 - 37.7 (20.3)"  "0.1 - 229.2 (39.4)"
[1] "hr=" "21" 
D57V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CD MUTATED         2        0        0        0         0         0
  PIK3CD WILD-TYPE      17       24       11        5         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
                  vv
clus               STAGE IS
  PIK3CD MUTATED          1
  PIK3CD WILD-TYPE       45
D57V3, multiclass
            clus
vv           PIK3CD MUTATED PIK3CD WILD-TYPE
  STAGE I                 2               17
  STAGE IA                0               24
  STAGE IB                0               11
  STAGE II                0                5
  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
  STAGE IS                1               45
[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 70 50  6
D57V4, multiclass
    clus
vv   PIK3CD MUTATED PIK3CD WILD-TYPE
  T1              3               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
  PIK3CD MUTATED    2     0
  PIK3CD WILD-TYPE 43    12
D57V5, multiclass
[1] "Remove cluster labels:" "PIK3CD MUTATED"        
clus
  PIK3CD MUTATED PIK3CD WILD-TYPE 
               2               55 
      TCGA-2G-AAEX       TCGA-2G-AAF1       TCGA-2G-AAF4       TCGA-2G-AAF6 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAF8       TCGA-2G-AAFG       TCGA-2G-AAFH       TCGA-2G-AAFI 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFJ       TCGA-2G-AAFL       TCGA-2G-AAFM       TCGA-2G-AAFN 
"PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" "PIK3CD WILD-TYPE" 
      TCGA-2G-AAFO       TCGA-2G-AAFV       TCGA-2G-AAFY       TCGA-2G-AAG0 
"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" 
D57V6, binary
                  cls
clus                 0   1
  PIK3CD MUTATED     2   0
  PIK3CD WILD-TYPE 110   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CD MUTATED      2    0
  PIK3CD WILD-TYPE  110    4
   clus
vv  PIK3CD MUTATED PIK3CD WILD-TYPE
  0              2              110
  1              0                4
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CD MUTATED       0                         0     3
  PIK3CD WILD-TYPE     4                         6   112
D57V7, multiclass
                           clus
vv                          PIK3CD MUTATED PIK3CD WILD-TYPE
  ASIAN                                  0                4
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  3              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"
D57V8, binary
                  cls
clus                 0   1
  PIK3CD MUTATED     0   3
  PIK3CD WILD-TYPE  11 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CD MUTATED      0    3
  PIK3CD WILD-TYPE   11  106
                        clus
vv                       PIK3CD MUTATED PIK3CD WILD-TYPE
  HISPANIC OR LATINO                  0               11
  NOT HISPANIC OR LATINO              3              106
[1] 2 2
[1] FALSE

Clustering(58) Variable = EPAS1 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  EPAS1 MUTATED     4   0
  EPAS1 WILD-TYPE 122   4
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              4             126 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              0               4 
$`EPAS1 MUTATED`
TCGA-2G-AAH4 TCGA-4K-AA1I TCGA-VF-A8A8 TCGA-XE-A8H4 
      125.69         0.10        37.18        18.38 

$`EPAS1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP 
       75.09       108.16        59.64       106.39       115.00       120.62 
TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY 
       59.28       124.57       128.94        61.45       170.33        80.94 
TCGA-2G-AAGZ TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.16        60.26        59.84        59.90        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H 
      131.21        70.59         2.73         0.13         3.52         7.00 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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         3.52        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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 
       40.01        34.22        65.98         0.46        53.03        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         8.32        12.92        20.12         6.90 
TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y TCGA-YU-A912 
       57.90        54.35        31.92        21.96         0.56         5.29 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA06 
       58.88         7.96        40.96         8.15        37.02        39.35 
TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       27.55        17.39        16.41        11.34        46.88        10.85 

  EPAS1 MUTATED EPAS1 WILD-TYPE 
           0.10            0.13 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         125.69          229.22 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         27.780          38.825 
[1] "0.1 - 125.7 (27.8)" "0.1 - 229.2 (38.8)"
[1] "hr="     "2.5e+07"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPAS1 MUTATED         0        3        0        1         0         0
  EPAS1 WILD-TYPE      19       21       11        4         5         1
                 vv
clus              STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  EPAS1 MUTATED           0         0          0          0          0        0
  EPAS1 WILD-TYPE         1         2          1          6          5       46
D58V3, multiclass
            clus
vv           EPAS1 MUTATED EPAS1 WILD-TYPE
  STAGE I                0              19
  STAGE IA               3              21
  STAGE IB               0              11
  STAGE II               1               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
  STAGE IS               0              46
[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 70 50  6
D58V4, multiclass
    clus
vv   EPAS1 MUTATED EPAS1 WILD-TYPE
  T1             3              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
  EPAS1 MUTATED    2     0
  EPAS1 WILD-TYPE 43    12
D58V5, multiclass
[1] "Remove cluster labels:" "EPAS1 MUTATED"         
clus
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              2              55 
     TCGA-2G-AAEW      TCGA-2G-AAEX      TCGA-2G-AAF1      TCGA-2G-AAF4 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAF6      TCGA-2G-AAF8      TCGA-2G-AAFG      TCGA-2G-AAFH 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFI      TCGA-2G-AAFJ      TCGA-2G-AAFL      TCGA-2G-AAFM 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAFN      TCGA-2G-AAFO      TCGA-2G-AAFV      TCGA-2G-AAFY 
"EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" "EPAS1 WILD-TYPE" 
     TCGA-2G-AAG0      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" 
D58V6, binary
                 cls
clus                0   1
  EPAS1 MUTATED     4   0
  EPAS1 WILD-TYPE 108   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      4    0
  EPAS1 WILD-TYPE  108    4
   clus
vv  EPAS1 MUTATED EPAS1 WILD-TYPE
  0             4             108
  1             0               4
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPAS1 MUTATED       0                         0     4
  EPAS1 WILD-TYPE     4                         6   111
D58V7, multiclass
                           clus
vv                          EPAS1 MUTATED EPAS1 WILD-TYPE
  ASIAN                                 0               4
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 4             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"
D58V8, binary
                 cls
clus                0   1
  EPAS1 MUTATED     0   4
  EPAS1 WILD-TYPE  11 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      0    4
  EPAS1 WILD-TYPE   11  105
                        clus
vv                       EPAS1 MUTATED EPAS1 WILD-TYPE
  HISPANIC OR LATINO                 0              11
  NOT HISPANIC OR LATINO             4             105
[1] 2 2
[1] FALSE

Clustering(59) Variable = DLC1 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 123   4
  DLC1 MUTATED DLC1 WILD-TYPE 
             3            127 
  DLC1 MUTATED DLC1 WILD-TYPE 
             0              4 
$`DLC1 MUTATED`
TCGA-2G-AAGJ TCGA-2X-A9D6 TCGA-SO-A8JP 
       75.09         0.13         3.52 

$`DLC1 WILD-TYPE`
TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
       20.32        30.35        38.30        59.70       102.35       122.40 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFL TCGA-2G-AAFM 
      191.31        36.99        14.14        14.56        17.16         9.57 
TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFV TCGA-2G-AAFY TCGA-2G-AAFZ TCGA-2G-AAG0 
       14.86        16.50        40.70        36.13        36.89        40.01 
TCGA-2G-AAG3 TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAG9 
       52.37        71.24        72.20        61.71        63.22        63.32 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG TCGA-2G-AAGI 
       68.22        72.85        68.38        79.76        67.96        92.09 
TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGS 
      108.16        59.64       106.39       115.00       120.62        59.28 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAGZ 
      124.57       128.94        61.45       170.33        80.94        60.16 
TCGA-2G-AAH0 TCGA-2G-AAH2 TCGA-2G-AAH3 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAHA 
       60.26        59.84        59.90       125.69        61.84        98.53 
TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT 
       59.74        59.80        59.80        91.43       176.15         6.08 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      122.50       212.65       161.72        95.67       229.22       184.41 
TCGA-2G-AAL7 TCGA-2G-AALP TCGA-2X-A9D5 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
      131.21        70.59         2.73         3.52         7.00         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C 
        4.83        20.68        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-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 
        3.65         5.06         0.16         0.82        28.14         6.87 
TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-AANI TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       18.38        40.01        34.22        65.98         0.46        53.03 
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         8.32        12.92        20.12 
TCGA-XY-A9T9 TCGA-YU-A90P TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A90Y 
        6.90        57.90        54.35        31.92        21.96         0.56 
TCGA-YU-A912 TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 
        5.29        58.88         7.96        40.96         8.15        37.02 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0E TCGA-ZM-AA0F TCGA-ZM-AA0H 
       39.35        27.55        17.39        16.41        11.34        46.88 
TCGA-ZM-AA0N 
       10.85 

  DLC1 MUTATED DLC1 WILD-TYPE 
          0.13           0.10 
  DLC1 MUTATED DLC1 WILD-TYPE 
         75.09         229.22 
  DLC1 MUTATED DLC1 WILD-TYPE 
          3.52          38.30 
[1] "0.1 - 75.1 (3.5)"   "0.1 - 229.2 (38.3)"
[1] "hr="     "9100000"
D59V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLC1 MUTATED         2        1        0        0         0         0
  DLC1 WILD-TYPE      17       23       11        5         5         1
                vv
clus             STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IS
  DLC1 MUTATED           0         0          0          0          0        0
  DLC1 WILD-TYPE         1         2          1          6          5       46
D59V3, multiclass
            clus
vv           DLC1 MUTATED DLC1 WILD-TYPE
  STAGE I               2             17
  STAGE IA              1             23
  STAGE IB              0             11
  STAGE II              0              5
  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
  STAGE IS              0             46
[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 70 50  6
D59V4, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  T1            3             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
  DLC1 MUTATED    2     0
  DLC1 WILD-TYPE 43    12
D59V5, multiclass
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2             55 
    TCGA-2G-AAEW     TCGA-2G-AAEX     TCGA-2G-AAF1     TCGA-2G-AAF4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAF6     TCGA-2G-AAF8     TCGA-2G-AAFG     TCGA-2G-AAFH 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAFI     TCGA-2G-AAFJ     TCGA-2G-AAFL     TCGA-2G-AAFM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAFN     TCGA-2G-AAFO     TCGA-2G-AAFV     TCGA-2G-AAFY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-2G-AAG0     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" 
D59V6, binary
                cls
clus               0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 109   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    0
  DLC1 WILD-TYPE  109    4
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            3            109
  1            0              4
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED       0                         1     2
  DLC1 WILD-TYPE     4                         5   113
D59V7, multiclass
                           clus
vv                          DLC1 MUTATED DLC1 WILD-TYPE
  ASIAN                                0              4
  BLACK OR AFRICAN AMERICAN            1              5
  WHITE                                2            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"
D59V8, binary
                cls
clus               0   1
  DLC1 MUTATED     0   3
  DLC1 WILD-TYPE  11 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      0    3
  DLC1 WILD-TYPE   11  106
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                0             11
  NOT HISPANIC OR LATINO            3            106
[1] 2 2
[1] FALSE
