[1] "ofn"        "-oTTHCA-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/THCA-TP/19775590/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/19898941/transformed.cor.cli.txt"

nPatients in clinical file=503, in cluster file=401, common to both=401
[1] "Reduce the number of clustering variables from 12 to 11."
[1]  11 401
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           240            161 
  BRAF MUTATED BRAF WILD-TYPE 
           240            161 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            34            367 
  NRAS MUTATED NRAS WILD-TYPE 
            34            367 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14            387 
  HRAS MUTATED HRAS WILD-TYPE 
            14            387 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              395 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              395 
[1] "NUP93 MUTATION ANALYSIS"
[1] 3
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             397 
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             397 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             396 
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             396 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             4            397 
  KRAS MUTATED KRAS WILD-TYPE 
             4            397 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            397 
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            397 
[1] "ITGAL MUTATION ANALYSIS"
[1] 3
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             397 
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             397 
[1] "TG MUTATION ANALYSIS"
[1] 3
  TG MUTATED TG WILD-TYPE 
          11          390 
  TG MUTATED TG WILD-TYPE 
          11          390 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             398 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             398 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 401 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=14,	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=354,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 401 columns, 1 survival variables, and 16 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"           "PATHOLOGIC_STAGE"        
 [3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
 [5] "PATHOLOGY_M_STAGE"        "GENDER"                  
 [7] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=71, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
117 136 131  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
117 136 131  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
117 136 131  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
117 136 131  15 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=59, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BRAF MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  BRAF MUTATED   230   9
  BRAF WILD-TYPE 156   5
  BRAF MUTATED BRAF WILD-TYPE 
           239            161 
  BRAF MUTATED BRAF WILD-TYPE 
             9              5 
$`BRAF MUTATED`
TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
       16.34        41.33         4.01        15.12        41.52        42.15 
TCGA-BJ-A28S TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PR 
       21.04        30.97        30.21        18.97        16.01        36.39 
TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A3ME 
       18.64        15.45        21.63        19.43        23.47        12.46 
TCGA-DE-A0XZ TCGA-DE-A0Y3 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13T 
       35.84        50.17         9.96        38.17       169.32        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       23.38        43.17         8.32        11.01       135.91        30.61 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       42.51        14.96         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
       10.09         7.82        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q3 
       33.96        31.99        34.85         8.78         8.42        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       33.93        37.48        36.46        35.11        35.90        33.53 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ 
       15.88        36.92        31.04        32.42        31.46        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 
       36.33        17.69        59.57        11.34        35.87        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       24.82        22.92        18.97         7.76        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A4UL TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DO-A1K0 
       17.23        30.87        26.93         3.12        15.81        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
        2.33        92.55        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 
       31.23        35.67        29.98        31.04         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EL-A3CL TCGA-EL-A3CM 
        0.16        14.96         7.69         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
      155.54       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP 
       37.94        57.01       139.86        98.53       108.36        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX 
       50.24       115.10        65.39       136.01        50.37       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
      101.13       139.99        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
      129.57       132.07        98.24        41.29       107.47        66.90 
TCGA-EL-A3ZQ TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       61.22        59.44        34.72        45.96        37.94        31.04 
TCGA-EL-A4K4 TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       53.36        24.30        27.06        18.18        20.91        48.49 
TCGA-EM-A22I TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2OX TCGA-EM-A2OZ 
       14.73        14.53        44.19        41.29        19.73        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AR 
       17.59        17.46        17.29        14.60        15.68        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O3 TCGA-EM-A3O7 
       27.95        23.77        21.01        17.49        14.50         7.33 
TCGA-EM-A3O8 TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G 
        0.49         5.33        26.37        22.45        24.46        81.93 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       77.56        70.42        65.29        63.45        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39O 
       52.60         2.66       106.09       107.41        84.89       100.57 
TCGA-ET-A39P TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       95.34        55.10        98.20        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DW TCGA-FE-A22Z 
      116.78        94.59        43.73        62.83        24.72        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FK-A3SB 
       66.77       112.80        81.83        85.15        85.68         4.11 
TCGA-FK-A3SH TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R7 TCGA-FY-A3R8 
       48.10        20.42        17.82        19.56        16.27        15.68 
TCGA-FY-A3RA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RI 
       18.08        15.16         1.35        12.53        17.00         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        18.51        16.90        17.23 
TCGA-J8-A3YE TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP 
       27.85        15.68        18.64        87.39        84.72        33.40 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83         9.50        36.10        32.45        30.21 

$`BRAF WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0ZA TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
       24.79        13.78        49.78        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28T 
       25.48        42.08        51.39         4.83        44.35        35.54 
TCGA-BJ-A28V TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
       32.45        11.08        18.38        16.57        20.48         7.04 
TCGA-BJ-A3F0 TCGA-BJ-A3PT TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       13.94        23.31        10.88        21.01         3.45        23.84 
TCGA-BJ-A45K TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A482 TCGA-CE-A484 
       23.18        12.66        12.30        12.79        10.68        12.43 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
       12.66        21.63        37.64        15.85        18.54        18.84 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL 
       48.79        18.58         8.71        52.37        44.98        17.59 
TCGA-DJ-A2PP TCGA-DJ-A2PX TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q8 
       30.58        28.96        34.36        37.74         6.77        39.09 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VM TCGA-DJ-A4UP 
       35.18        16.41        32.81        36.33        27.62        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 
       27.06        35.54        35.38        54.90        47.21        66.38 
TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D4 
        0.39        97.74       106.62         4.18        79.50        69.57 
TCGA-EL-A3D5 TCGA-EL-A3GO TCGA-EL-A3GW TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
       57.11        64.87        50.20        49.32        33.50        43.36 
TCGA-EL-A3T0 TCGA-EL-A3T2 TCGA-EL-A3T9 TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
      142.52        32.48         5.72        82.82        78.97        51.78 
TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KD 
       53.06        60.16        57.47        30.51        44.15        43.59 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       23.90        26.86        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
       57.01        54.08        14.50        15.75        10.45        10.65 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        47.57        17.88        13.18        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        13.64        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN 
       40.34        32.32        22.52        30.94        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3FL TCGA-EM-A3FN TCGA-EM-A3FP 
       13.38         8.35        29.72        47.38        12.07        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O6 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       16.18        15.02        15.06         9.24        13.91        38.66 
TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A2N1 TCGA-ET-A2N5 
       21.34        21.53        13.68        81.70        54.35        80.88 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BN TCGA-ET-A3DQ 
       33.24       108.46       123.32        94.13        28.24        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A3PD 
       80.58        66.84       166.62        40.21        33.17        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FY-A2QD TCGA-FY-A3I5 
       71.08         1.05        13.28         0.92         1.25         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3R6 TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-FY-A3WA 
        0.99        16.14        13.91        16.57         0.76        17.06 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A4HW 
       21.67        12.46        43.17        27.19         2.60 

  BRAF MUTATED BRAF WILD-TYPE 
          0.16           0.39 
  BRAF MUTATED BRAF WILD-TYPE 
        169.32         166.62 
  BRAF MUTATED BRAF WILD-TYPE 
         33.96          23.84 
[1] "0.2 - 169.3 (34.0)" "0.4 - 166.6 (23.8)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  BRAF MUTATED       131       18        60        0        26         4
  BRAF WILD-TYPE     100       25        24        2         7         2
D1V3, multiclass
           clus
vv          BRAF MUTATED BRAF WILD-TYPE
  STAGE I            131            100
  STAGE II            18             25
  STAGE III           60             24
  STAGE IV             0              2
  STAGE IVA           26              7
  STAGE IVC            4              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  BRAF MUTATED   69 66 91 13
  BRAF WILD-TYPE 48 70 40  2
D1V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           69             48
  T2           66             70
  T3           91             40
  T4           13              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus               0   1
  BRAF MUTATED   100 119
  BRAF WILD-TYPE  90  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    100  119
  BRAF WILD-TYPE   90   51
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0          100             90
  1          119             51
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus               0   1
  BRAF MUTATED   142   5
  BRAF WILD-TYPE  80   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    142    5
  BRAF WILD-TYPE   80    2
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0          142             80
  1            5              2
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  BRAF MUTATED   173  67
  BRAF WILD-TYPE 125  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    173   67
  BRAF WILD-TYPE  125   36
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE          173            125
  MALE             67             36
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  BRAF MUTATED    98 135
  BRAF WILD-TYPE  63  88
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     98  135
  BRAF WILD-TYPE   63   88
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            98             63
  YES          135             88
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  BRAF MUTATED                2                                           193
  BRAF WILD-TYPE              3                                            88
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  BRAF MUTATED                                                                       17
  BRAF WILD-TYPE                                                                     68
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  BRAF MUTATED                                                                    28
  BRAF WILD-TYPE                                                                   2
D1V9, multiclass
                                                                        clus
vv                                                                       BRAF MUTATED
  OTHER  SPECIFY                                                                    2
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   193
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           17
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              28
                                                                        clus
vv                                                                       BRAF WILD-TYPE
  OTHER  SPECIFY                                                                      3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      88
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             68
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                cls
clus               0   1
  BRAF MUTATED   205   8
  BRAF WILD-TYPE 131   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    205    8
  BRAF WILD-TYPE  131    7
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO           205            131
  YES            8              7
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  BRAF MUTATED             81                      11  143                   0
  BRAF WILD-TYPE           23                       0  129                   1
D1V11, multiclass
                         clus
vv                        BRAF MUTATED BRAF WILD-TYPE
  MINIMAL (T3)                      81             23
  MODERATE/ADVANCED (T4A)           11              0
  NONE                             143            129
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED   185  25   3  15
  BRAF WILD-TYPE 129  12   0   7
D1V12, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0          185            129
  R1           25             12
  R2            3              0
  RX           15              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
D1V14, binary
                cls
clus               0   1
  BRAF MUTATED   110 127
  BRAF WILD-TYPE  71  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    110  127
  BRAF WILD-TYPE   71   84
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  MULTIFOCAL          110             71
  UNIFOCAL            127             84
[1] 2 2
[1] FALSE
D1V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED      24                        11   173
  BRAF WILD-TYPE    14                         7    92
D1V16, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                               24             14
  BLACK OR AFRICAN AMERICAN           11              7
  WHITE                              173             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V17, binary
                cls
clus               0   1
  BRAF MUTATED    22 184
  BRAF WILD-TYPE   9 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     22  184
  BRAF WILD-TYPE    9  107
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO               22              9
  NOT HISPANIC OR LATINO          184            107
[1] 2 2
[1] FALSE

Clustering(2) Variable = NRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    34   0
  NRAS WILD-TYPE 352  14
  NRAS MUTATED NRAS WILD-TYPE 
            34            366 
  NRAS MUTATED NRAS WILD-TYPE 
             0             14 
$`NRAS MUTATED`
TCGA-BJ-A0ZA TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A3PT TCGA-BJ-A45F TCGA-BJ-A45G 
       18.87        18.38        16.57        23.31         3.45        23.84 
TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-EL-A3GW 
        8.71        44.98        30.58        16.41        36.33        50.20 
TCGA-EL-A3T2 TCGA-EL-A3ZH TCGA-EL-A4K2 TCGA-EL-A4K6 TCGA-EL-A4KI TCGA-EM-A22J 
       32.48        78.97        30.51        44.15        23.90        14.50 
TCGA-EM-A22L TCGA-EM-A22Q TCGA-EM-A2CN TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A3AP 
       10.45        14.24        23.51        13.64        48.46         8.35 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4G1 TCGA-ET-A25I TCGA-FY-A3NP 
       13.91        38.66        21.34        13.68        81.70        16.14 
TCGA-FY-A3R9 TCGA-FY-A3W9 TCGA-H2-A2K9 TCGA-J8-A3O0 
       16.57         0.76        21.67        43.17 

$`NRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB 
       24.79        13.78        49.78        16.34        41.33         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73        25.48        15.12        42.08        51.39 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       41.52         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N9 TCGA-BJ-A2NA 
       32.45        30.97        11.08        30.21        20.48        18.97 
TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PU TCGA-BJ-A45D 
        7.04        16.01        13.94        36.39        18.64        10.88 
TCGA-BJ-A45E TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       21.01        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
       12.66        12.30        12.79        12.46        10.68        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       18.54        18.84         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
       18.58        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL 
       11.01       135.91        30.61        42.51        14.96        17.59 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        6.02        42.58        47.41        17.56        10.09         7.82 
TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV 
       35.41        27.45        26.20        38.83        33.96        31.99 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85        28.96         8.78         8.42        34.36        37.74 
TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 
        6.77        40.24        33.93        37.48        36.46        35.11 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
       39.09        35.90        33.53        35.18        15.88        36.92 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       31.04        32.42        31.46        19.56        36.33        32.81 
TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA 
       17.69        59.57        11.34        35.87        23.21        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL 
       22.92        18.97         7.76        36.43        24.76        17.23 
TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 
       27.62        30.87        21.34        27.06        26.93        35.54 
TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM 
        3.12        15.81        35.38        54.90        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 
       92.55        47.21        66.38        80.52        63.19        52.44 
TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 
       39.95        31.23        35.67        29.98        31.04         3.02 
TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M 
       25.45         0.16        14.96         7.69         0.39         0.39 
TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR 
       31.66        26.73       155.54        97.74       158.83         7.66 
TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX 
       45.53        60.95       157.15        37.94        57.01       106.62 
TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 
        4.18        79.50       139.86        98.53        69.57        57.11 
TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS 
      108.36        64.87        49.51        50.24       115.10        65.39 
TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
      136.01        50.37       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      142.52       129.57       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ 
        5.72        66.90        82.82        51.78        53.06        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       60.16        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS 
       31.04        53.36        43.59        24.30        27.06        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        48.49        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22K TCGA-EM-A22M 
       78.61        57.01        54.08        14.73        15.75        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       10.65        44.19        41.29        47.57        17.88        13.18 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
        6.05         2.99        12.30        13.15        22.16        40.34 
TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 
       19.73        32.32        33.96        17.59        17.46        17.29 
TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN 
       14.60        22.52        30.94        15.68        14.14        33.07 
TCGA-EM-A3AO TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
       13.38        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A4FM 
       14.50        15.06         7.33         0.49         9.24         5.33 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J 
       26.37        22.45        21.53        24.46        81.93        77.56 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       70.42        65.29        63.45        58.75        37.25        52.60 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       54.35         2.66        80.88        33.24       106.09       107.41 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
      108.46        84.89       123.32       100.57        95.34        94.13 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        98.20        28.24        50.40        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       62.83       166.62        24.72        40.21        33.17        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       66.77       112.80        81.83        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON 
        1.25        20.42        17.82         7.82         0.99        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3WA TCGA-FY-A40K 
       13.91        16.27        15.68        18.08        17.06        15.16 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
        1.35        12.53        17.00        12.46         2.99        20.05 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O1 
       48.92        47.41        18.51        16.90        17.23        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68        18.64        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         9.50        36.10        32.45        30.21 

  NRAS MUTATED NRAS WILD-TYPE 
          0.76           0.16 
  NRAS MUTATED NRAS WILD-TYPE 
         81.70         169.32 
  NRAS MUTATED NRAS WILD-TYPE 
        21.505         32.155 
[1] "0.8 - 81.7 (21.5)"  "0.2 - 169.3 (32.2)"
[1] "hr="     "2.7e+07"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NRAS MUTATED        22        6         4        1         0         1
  NRAS WILD-TYPE     209       37        80        1        33         5
D2V3, multiclass
           clus
vv          NRAS MUTATED NRAS WILD-TYPE
  STAGE I             22            209
  STAGE II             6             37
  STAGE III            4             80
  STAGE IV             1              1
  STAGE IVA            0             33
  STAGE IVC            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAS MUTATED    10  17   6   1
  NRAS WILD-TYPE 107 119 125  14
D2V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1           10            107
  T2           17            119
  T3            6            125
  T4            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                cls
clus               0   1
  NRAS MUTATED    27   5
  NRAS WILD-TYPE 163 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     27    5
  NRAS WILD-TYPE  163  165
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           27            163
  1            5            165
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  NRAS MUTATED    17   1
  NRAS WILD-TYPE 205   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     17    1
  NRAS WILD-TYPE  205    6
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           17            205
  1            1              6
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  NRAS MUTATED    25   9
  NRAS WILD-TYPE 273  94
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     25    9
  NRAS WILD-TYPE  273   94
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           25            273
  MALE              9             94
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  NRAS MUTATED    16  17
  NRAS WILD-TYPE 145 206
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     16   17
  NRAS WILD-TYPE  145  206
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            16            145
  YES           17            206
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NRAS MUTATED                0                                            14
  NRAS WILD-TYPE              5                                           267
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NRAS MUTATED                                                                       20
  NRAS WILD-TYPE                                                                     65
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NRAS MUTATED                                                                     0
  NRAS WILD-TYPE                                                                  30
D2V9, multiclass
                                                                        clus
vv                                                                       NRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                    14
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           20
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       NRAS WILD-TYPE
  OTHER  SPECIFY                                                                      5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     267
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             65
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                cls
clus               0   1
  NRAS MUTATED    28   1
  NRAS WILD-TYPE 308  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     28    1
  NRAS WILD-TYPE  308   14
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            28            308
  YES            1             14
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NRAS MUTATED              4                       0   27                   0
  NRAS WILD-TYPE          100                      11  245                   1
D2V11, multiclass
                         clus
vv                        NRAS MUTATED NRAS WILD-TYPE
  MINIMAL (T3)                       4            100
  MODERATE/ADVANCED (T4A)            0             11
  NONE                              27            245
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    27   1   0   1
  NRAS WILD-TYPE 287  36   3  21
D2V12, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           27            287
  R1            1             36
  R2            0              3
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
D2V14, binary
                cls
clus               0   1
  NRAS MUTATED    13  21
  NRAS WILD-TYPE 168 190
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13   21
  NRAS WILD-TYPE  168  190
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  MULTIFOCAL           13            168
  UNIFOCAL             21            190
[1] 2 2
[1] FALSE
D2V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         0    21
  NRAS WILD-TYPE    38                        18   244
D2V16, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                               21            244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V17, binary
                cls
clus               0   1
  NRAS MUTATED     5  18
  NRAS WILD-TYPE  26 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5   18
  NRAS WILD-TYPE   26  273
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                5             26
  NOT HISPANIC OR LATINO           18            273
[1] 2 2
[1] FALSE

Clustering(3) Variable = HRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    13   1
  HRAS WILD-TYPE 373  13
  HRAS MUTATED HRAS WILD-TYPE 
            14            386 
  HRAS MUTATED HRAS WILD-TYPE 
             1             13 
$`HRAS MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A45D TCGA-DJ-A13M TCGA-DJ-A2QB 
       49.78        51.39         7.04        10.88        48.79        35.18 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EM-A22K TCGA-EM-A2CK 
       47.21        79.50        60.16        57.47        15.75        17.88 
TCGA-ET-A2N5 TCGA-ET-A39I 
       80.88        33.24 

$`HRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB 
       24.79        13.78        16.34        41.33        18.87         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Z 
       11.57        16.73        25.48        15.12        42.08        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       30.97        11.08        30.21        18.38        16.57        20.48 
TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU 
       18.97        16.01        13.94        36.39        23.31        18.64 
TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K 
       21.01         3.45        23.84        15.45        21.63        23.18 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
       19.43        23.47        12.66        12.30        12.79        12.46 
TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68        12.43        12.66        35.84        21.63        50.17 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13O 
       37.64        15.85        18.54        18.84         9.96        38.17 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32        18.58         8.71        56.19        23.38        43.17 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       52.37         8.32        11.01       135.91        30.61        44.98 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
       42.51        14.96        17.59         6.02        42.58        47.41 
TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR 
       17.56        10.09         7.82        30.58        35.41        27.45 
TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX 
       26.20        38.83        33.96        31.99        34.85        28.96 
TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 
        8.78         8.42        34.36        37.74         6.77        40.24 
TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 
       33.93        37.48        36.46        35.11        39.09        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       33.53        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        35.87        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       30.87        21.34        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       35.67        29.98        31.04         3.02        25.45         0.16 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3D0 
      157.15        37.94        57.01       106.62         4.18       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ 
       66.90        82.82        78.97        51.78        53.06        61.22 
TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 
       59.44        34.72        45.96        37.94        31.04        30.51 
TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI 
       53.36        44.15        43.59        24.30        27.06        23.90 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA 
       26.86        18.18        20.91        48.49        18.05        19.79 
TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J 
       19.46        78.61        57.01        54.08        14.73        14.50 
TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q 
       10.45        14.53        10.65        44.19        41.29        14.24 
TCGA-EM-A2CJ TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       47.57        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       21.01        12.07        17.49        17.39        16.18        15.02 
TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA 
       14.50        15.06         7.33         0.49         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
       38.66        21.34         5.33        26.37        22.45        21.53 
TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       24.46        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       65.29        63.45        58.75        37.25        52.60        54.35 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
        2.66       106.09       107.41       108.46        84.89       123.32 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
      100.57        95.34        94.13        55.10        98.20        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
       50.40        79.10        76.64         5.79        87.62        77.82 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       75.42        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
       40.21        33.17        73.74        71.44        31.59        79.69 
TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A 
       24.69        68.22       117.40        66.77       112.80        81.83 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD 
       85.15        85.68        78.77        71.08         4.11         1.05 
TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
       13.28         0.92        48.10         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        7.82         0.99        16.14        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K 
       15.68        16.57        18.08         0.76        17.06        15.16 
TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI 
        1.35        12.53        17.00        21.67        12.46         2.99 
TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
       20.05        48.92        47.41        18.51        16.90        17.23 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 
       43.17        27.19        27.85         2.60        15.68        18.64 
TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 
       87.39        84.72        33.40        21.83         9.50        36.10 
TCGA-MK-A4N7 TCGA-MK-A4N9 
       32.45        30.21 

  HRAS MUTATED HRAS WILD-TYPE 
          7.04           0.16 
  HRAS MUTATED HRAS WILD-TYPE 
         80.88         169.32 
  HRAS MUTATED HRAS WILD-TYPE 
        48.000         30.905 
[1] "7.0 - 80.9 (48.0)"  "0.2 - 169.3 (30.9)"
[1] "hr=" "1.8"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  HRAS MUTATED         8        1         2        0         2         1
  HRAS WILD-TYPE     223       42        82        2        31         5
D3V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              8            223
  STAGE II             1             42
  STAGE III            2             82
  STAGE IV             0              2
  STAGE IVA            2             31
  STAGE IVC            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HRAS MUTATED     5   6   3   0
  HRAS WILD-TYPE 112 130 128  15
D3V4, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T1            5            112
  T2            6            130
  T3            3            128
  T4            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                cls
clus               0   1
  HRAS MUTATED     8   4
  HRAS WILD-TYPE 182 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      8    4
  HRAS WILD-TYPE  182  166
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            8            182
  1            4            166
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus               0   1
  HRAS MUTATED     8   1
  HRAS WILD-TYPE 214   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      8    1
  HRAS WILD-TYPE  214    6
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            8            214
  1            1              6
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  HRAS MUTATED    10   4
  HRAS WILD-TYPE 288  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     10    4
  HRAS WILD-TYPE  288   99
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           10            288
  MALE              4             99
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus               0   1
  HRAS MUTATED     2  10
  HRAS WILD-TYPE 159 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      2   10
  HRAS WILD-TYPE  159  213
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             2            159
  YES           10            213
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  HRAS MUTATED                0                                             6
  HRAS WILD-TYPE              5                                           275
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  HRAS MUTATED                                                                        8
  HRAS WILD-TYPE                                                                     77
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  HRAS MUTATED                                                                     0
  HRAS WILD-TYPE                                                                  30
D3V9, multiclass
                                                                        clus
vv                                                                       HRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            8
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       HRAS WILD-TYPE
  OTHER  SPECIFY                                                                      5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     275
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             77
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                cls
clus               0   1
  HRAS MUTATED    12   0
  HRAS WILD-TYPE 324  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     12    0
  HRAS WILD-TYPE  324   15
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO            12            324
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  HRAS MUTATED              2                       0   11                   0
  HRAS WILD-TYPE          102                      11  261                   1
D3V11, multiclass
                         clus
vv                        HRAS MUTATED HRAS WILD-TYPE
  MINIMAL (T3)                       2            102
  MODERATE/ADVANCED (T4A)            0             11
  NONE                              11            261
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HRAS MUTATED     9   2   0   2
  HRAS WILD-TYPE 305  35   3  20
D3V12, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            9            305
  R1            2             35
  R2            0              3
  RX            2             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
D3V14, binary
                cls
clus               0   1
  HRAS MUTATED     6   8
  HRAS WILD-TYPE 175 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      6    8
  HRAS WILD-TYPE  175  203
            clus
vv           HRAS MUTATED HRAS WILD-TYPE
  MULTIFOCAL            6            175
  UNIFOCAL              8            203
[1] 2 2
[1] FALSE
D3V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       2                         2     8
  HRAS WILD-TYPE    36                        16   257
D3V16, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            2             16
  WHITE                                8            257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V17, binary
                cls
clus               0   1
  HRAS MUTATED     0  12
  HRAS WILD-TYPE  31 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   12
  HRAS WILD-TYPE   31  279
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO           12            279
[1] 2 2
[1] FALSE

Clustering(4) Variable = EIF1AX MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  EIF1AX MUTATED     5   1
  EIF1AX WILD-TYPE 381  13
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              394 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               1               13 
$`EIF1AX MUTATED`
TCGA-BJ-A0ZG TCGA-EL-A3CO TCGA-EM-A1YA TCGA-EM-A2CL TCGA-EM-A3FN TCGA-EM-A4FV 
       25.48        97.74        19.79        13.18        12.07        24.46 

$`EIF1AX WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        11.57        16.73        15.12        42.08        51.39 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       41.52         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        30.97        11.08        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64        10.88        21.01         3.45        23.84 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
       12.30        12.79        12.46        10.68        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.84         9.96        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        35.87        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       35.67        29.98        31.04         3.02        25.45         0.16 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
      155.54       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ 
       66.90        82.82        78.97        51.78        53.06        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       60.16        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG 
       31.04        30.51        53.36        44.15        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       18.05        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CN TCGA-EM-A2CO 
       41.29        14.24        47.57        17.88        23.51         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV 
        2.99        12.30        13.64        48.46        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       40.34        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       23.77        47.38        21.01        17.49        17.39        16.18 
TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 
       15.02        14.50        15.06         7.33         0.49         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ 
       13.91        38.66        21.34         5.33        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K 
       21.53        13.68        81.93        81.70        77.56        70.42 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       65.29        63.45        58.75        37.25        52.60        54.35 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       98.20        28.24        50.40        79.10        76.64         5.79 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       87.62        77.82        75.42        46.65        52.47       116.78 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       94.59        84.85        80.58        66.84        43.73        62.83 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 
      166.62        24.72        40.21        33.17        73.74        71.44 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        79.69        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 
      112.80        81.83        85.15        85.68        78.77        71.08 
TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD 
        4.11         1.05        13.28         0.92        48.10         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON 
       20.42        17.82         7.82         0.99        16.14        19.56 
TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 
       13.91        16.27        15.68        16.57        18.08         0.76 
TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 
       17.06        15.16         1.35        12.53        17.00        21.67 
TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       12.46         2.99        20.05        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW 
       16.90        17.23        43.17        27.19        27.85         2.60 
TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET 
       15.68        18.64        87.39        84.72        33.40        21.83 
TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
        9.50        36.10        32.45        30.21 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
           12.07             0.16 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           97.74           169.32 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          22.125           31.135 
[1] "12.1 - 97.7 (22.1)" "0.2 - 169.3 (31.1)"
[1] "hr=" "6.9"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  EIF1AX MUTATED         4        1         1        0         0         0
  EIF1AX WILD-TYPE     227       42        83        2        33         6
D4V3, multiclass
           clus
vv          EIF1AX MUTATED EIF1AX WILD-TYPE
  STAGE I                4              227
  STAGE II               1               42
  STAGE III              1               83
  STAGE IV               0                2
  STAGE IVA              0               33
  STAGE IVC              0                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF1AX MUTATED     2   2   2   0
  EIF1AX WILD-TYPE 115 134 129  15
D4V4, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  T1              2              115
  T2              2              134
  T3              2              129
  T4              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     3   1
  EIF1AX WILD-TYPE 187 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    1
  EIF1AX WILD-TYPE  187  169
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              3              187
  1              1              169
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     2   0
  EIF1AX WILD-TYPE 220   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      2    0
  EIF1AX WILD-TYPE  220    7
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              2              220
  1              0                7
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     3   3
  EIF1AX WILD-TYPE 295 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    3
  EIF1AX WILD-TYPE  295  100
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              3              295
  MALE                3              100
[1] 2 2
[1] FALSE
D4V8, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     4   2
  EIF1AX WILD-TYPE 157 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      4    2
  EIF1AX WILD-TYPE  157  221
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               4              157
  YES              2              221
[1] 2 2
[1] FALSE
                  vv
clus               OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  EIF1AX MUTATED                0                                             2
  EIF1AX WILD-TYPE              5                                           279
                  vv
clus               THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  EIF1AX MUTATED                                                                        4
  EIF1AX WILD-TYPE                                                                     81
                  vv
clus               THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  EIF1AX MUTATED                                                                     0
  EIF1AX WILD-TYPE                                                                  30
D4V9, multiclass
                                                                        clus
vv                                                                       EIF1AX MUTATED
  OTHER  SPECIFY                                                                      0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 0
                                                                        clus
vv                                                                       EIF1AX WILD-TYPE
  OTHER  SPECIFY                                                                        5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               81
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                  30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     6   0
  EIF1AX WILD-TYPE 330  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      6    0
  EIF1AX WILD-TYPE  330   15
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               6              330
  YES              0               15
[1] 2 2
[1] FALSE
                  vv
clus               MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  EIF1AX MUTATED              1                       0    5
  EIF1AX WILD-TYPE          103                      11  267
                  vv
clus               VERY ADVANCED (T4B)
  EIF1AX MUTATED                     0
  EIF1AX WILD-TYPE                   1
D4V11, multiclass
                         clus
vv                        EIF1AX MUTATED EIF1AX WILD-TYPE
  MINIMAL (T3)                         1              103
  MODERATE/ADVANCED (T4A)              0               11
  NONE                                 5              267
  VERY ADVANCED (T4B)                  0                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF1AX MUTATED     4   1   0   1
  EIF1AX WILD-TYPE 310  36   3  21
D4V12, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  R0              4              310
  R1              1               36
  R2              0                3
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
D4V14, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     3   2
  EIF1AX WILD-TYPE 178 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    2
  EIF1AX WILD-TYPE  178  209
            clus
vv           EIF1AX MUTATED EIF1AX WILD-TYPE
  MULTIFOCAL              3              178
  UNIFOCAL                2              209
[1] 2 2
[1] FALSE
D4V15, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF1AX MUTATED       0                         0     2
  EIF1AX WILD-TYPE    38                        18   263
D4V16, multiclass
[1] "Remove cluster labels:" "EIF1AX MUTATED"        
clus
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               2              319 
      TCGA-BJ-A0YZ       TCGA-BJ-A0Z2       TCGA-BJ-A0Z3       TCGA-BJ-A0Z9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A0ZA       TCGA-BJ-A0ZB       TCGA-BJ-A0ZC       TCGA-BJ-A0ZE 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A0ZH       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y       TCGA-BJ-A18Z 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R       TCGA-BJ-A28S 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28X       TCGA-BJ-A28Z 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A290       TCGA-BJ-A2N7       TCGA-BJ-A2N8       TCGA-BJ-A2N9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A2NA       TCGA-BJ-A2P4       TCGA-BJ-A3EZ       TCGA-BJ-A3F0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A3PR       TCGA-BJ-A3PT       TCGA-BJ-A3PU       TCGA-BJ-A45D 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A45E       TCGA-BJ-A45F       TCGA-BJ-A45G       TCGA-BJ-A45I 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-BJ-A45J       TCGA-BJ-A45K       TCGA-BJ-A4O8       TCGA-BJ-A4O9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-CE-A13K       TCGA-CE-A27D       TCGA-CE-A3MD       TCGA-CE-A3ME 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-CE-A482       TCGA-CE-A484       TCGA-CE-A485       TCGA-DE-A0XZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DE-A0Y2       TCGA-DE-A0Y3       TCGA-DE-A2OL       TCGA-DE-A3KN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DE-A4M8       TCGA-DE-A4M9       TCGA-DJ-A13L       TCGA-DJ-A13M 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A13O       TCGA-DJ-A13P       TCGA-DJ-A13R       TCGA-DJ-A13S 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A13T       TCGA-DJ-A13U       TCGA-DJ-A13W       TCGA-DJ-A1QD 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A1QE       TCGA-DJ-A1QF       TCGA-DJ-A1QG       TCGA-DJ-A1QH 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A1QI       TCGA-DJ-A1QM       TCGA-DJ-A1QO       TCGA-DJ-A1QQ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PN       TCGA-DJ-A2PO       TCGA-DJ-A2PQ       TCGA-DJ-A2PR 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PS       TCGA-DJ-A2PT       TCGA-DJ-A2PU       TCGA-DJ-A2PV 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2PW       TCGA-DJ-A2PX       TCGA-DJ-A2PY       TCGA-DJ-A2PZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2Q0       TCGA-DJ-A2Q1       TCGA-DJ-A2Q2       TCGA-DJ-A2Q3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2Q4       TCGA-DJ-A2Q5       TCGA-DJ-A2Q6       TCGA-DJ-A2Q7 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A2Q9       TCGA-DJ-A2QA       TCGA-DJ-A2QB       TCGA-DJ-A3UK 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UM       TCGA-DJ-A3UN       TCGA-DJ-A3UO       TCGA-DJ-A3UQ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UR       TCGA-DJ-A3US       TCGA-DJ-A3UT       TCGA-DJ-A3UU 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3UW       TCGA-DJ-A3UX       TCGA-DJ-A3UY       TCGA-DJ-A3V7 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3VE       TCGA-DJ-A3VF       TCGA-DJ-A3VJ       TCGA-DJ-A3VK 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3VL       TCGA-DJ-A3VM       TCGA-DJ-A4UL       TCGA-DJ-A4UP 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A4UT       TCGA-DJ-A4UW       TCGA-DJ-A4V0       TCGA-DJ-A4V4 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A4V5       TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-DO-A2HM 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3DY       TCGA-E3-A3DZ       TCGA-E3-A3E0       TCGA-E3-A3E1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3E2       TCGA-E3-A3E3       TCGA-E3-A3E5       TCGA-E8-A242 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A2EA       TCGA-E8-A413       TCGA-E8-A415       TCGA-E8-A418 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A419       TCGA-E8-A433       TCGA-E8-A436       TCGA-E8-A437 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A44K       TCGA-E8-A44M       TCGA-EL-A3CL       TCGA-EL-A3CM 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CN       TCGA-EL-A3CP       TCGA-EL-A3CR       TCGA-EL-A3CS 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CT       TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CX       TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3D1       TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GO       TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GS       TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GX       TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H2       TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H7       TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3MY       TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T0       TCGA-EL-A3T1       TCGA-EL-A3T2       TCGA-EL-A3T3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T6       TCGA-EL-A3T7       TCGA-EL-A3T8       TCGA-EL-A3T9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3TA       TCGA-EL-A3TB       TCGA-EL-A3ZH       TCGA-EL-A3ZK 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3ZN       TCGA-EL-A3ZQ       TCGA-EL-A3ZR       TCGA-EL-A3ZT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4JV       TCGA-EL-A4JW       TCGA-EL-A4JX       TCGA-EL-A4JZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4K0       TCGA-EL-A4K2       TCGA-EL-A4K4       TCGA-EL-A4K6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4KD       TCGA-EL-A4KG       TCGA-EL-A4KH       TCGA-EL-A4KI 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EM-A22M       TCGA-EM-A22O       TCGA-EM-A2OV       TCGA-EM-A3AI 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25G       TCGA-ET-A25I       TCGA-ET-A25J       TCGA-ET-A25K 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25O       TCGA-ET-A25R       TCGA-ET-A2MY       TCGA-ET-A2MZ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A2N0       TCGA-ET-A2N1       TCGA-ET-A2N4       TCGA-ET-A2N5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39I       TCGA-ET-A39J       TCGA-ET-A39K       TCGA-ET-A39M 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39N       TCGA-ET-A39O       TCGA-ET-A39P       TCGA-ET-A39R 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39S       TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BO 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BP       TCGA-ET-A3BQ       TCGA-ET-A3BS       TCGA-ET-A3BT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BU       TCGA-ET-A3BV       TCGA-ET-A3BW       TCGA-ET-A3BX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DO       TCGA-ET-A3DP       TCGA-ET-A3DQ       TCGA-ET-A3DR 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DS       TCGA-ET-A3DT       TCGA-ET-A3DU       TCGA-ET-A3DV 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DW       TCGA-ET-A40S       TCGA-ET-A4KN       TCGA-FE-A22Z 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A230       TCGA-FE-A231       TCGA-FE-A232       TCGA-FE-A233 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A234       TCGA-FE-A235       TCGA-FE-A236       TCGA-FE-A237 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A23A       TCGA-FE-A3PB       TCGA-FE-A3PC       TCGA-FE-A3PD 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FK-A3S3       TCGA-FK-A3SB       TCGA-FK-A3SD       TCGA-FK-A3SE 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FK-A3SG       TCGA-FK-A3SH       TCGA-FY-A2QD       TCGA-FY-A3BL 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3I4       TCGA-FY-A3I5       TCGA-FY-A3NM       TCGA-FY-A3NP 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3ON       TCGA-FY-A3R6       TCGA-FY-A3R7       TCGA-FY-A3R8 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3R9       TCGA-FY-A3RA       TCGA-FY-A3W9       TCGA-FY-A3WA 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A40K       TCGA-FY-A4B3       TCGA-GE-A2C6       TCGA-H2-A26U 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-H2-A2K9       TCGA-H2-A3RH       TCGA-H2-A3RI       TCGA-H2-A421 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-IM-A3EB       TCGA-IM-A3ED       TCGA-IM-A3U2       TCGA-IM-A3U3 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-J8-A3NZ       TCGA-J8-A3O0       TCGA-J8-A3O1       TCGA-J8-A3YE 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-J8-A4HW       TCGA-KS-A41J       TCGA-KS-A4I5       TCGA-KS-A4I9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-KS-A4IB       TCGA-L6-A4EP       TCGA-L6-A4ET       TCGA-L6-A4EU 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-MK-A4N6       TCGA-MK-A4N7       TCGA-MK-A4N9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
D4V17, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   2
  EIF1AX WILD-TYPE  31 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    2
  EIF1AX WILD-TYPE   31  289
                        clus
vv                       EIF1AX MUTATED EIF1AX WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              2              289
[1] 2 2
[1] FALSE

Clustering(5) Variable = NUP93 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  NUP93 MUTATED     4   0
  NUP93 WILD-TYPE 382  14
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             396 
  NUP93 MUTATED NUP93 WILD-TYPE 
              0              14 
$`NUP93 MUTATED`
TCGA-BJ-A191 TCGA-DJ-A2Q4 TCGA-EM-A4FQ TCGA-L6-A4EU 
        4.83        33.93        22.45         9.50 

$`NUP93 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       51.39        41.52        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        30.97        11.08        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64        10.88        21.01         3.45        23.84 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
       12.30        12.79        12.46        10.68        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.84         9.96        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       34.36        37.74         6.77        40.24        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       35.87        23.21        24.82        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       29.98        31.04         3.02        25.45         0.16        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69         0.39         0.39        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
       97.74       158.83         7.66        45.53        60.95       157.15 
TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 
       37.94        57.01       106.62         4.18        79.50       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        69.57        57.11       108.36        64.87        49.51 
TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW 
       50.24       115.10        65.39       136.01        50.37        50.20 
TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 
      147.75       101.13       139.99        49.32        33.50        43.36 
TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX 
       49.71        83.57       139.00       150.48       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       17.52        52.50        29.65       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ 
       66.90        82.82        78.97        51.78        53.06        61.22 
TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ 
       60.16        59.44        57.47        34.72        45.96        37.94 
TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG 
       31.04        30.51        53.36        44.15        43.59        24.30 
TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV 
       27.06        23.90        26.86        18.18        20.91        48.49 
TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       18.05        19.79        19.46        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT 
       23.51         6.05         2.99        12.30        13.64        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK 
        7.33         0.49         9.24        13.91        38.66        21.34 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        21.53        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
       81.70        77.56        70.42        65.29        63.45        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       37.25        52.60        54.35         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
       66.84        43.73        62.83       166.62        24.72        40.21 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       33.17        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
       68.22       117.40        66.77       112.80        81.83        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
        0.92        48.10         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        0.99        16.14        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 
       16.57        18.08         0.76        17.06        15.16         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 
       48.92        47.41        18.51        16.90        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 
       27.19        27.85         2.60        15.68        18.64        87.39 
TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       84.72        33.40        21.83        36.10        32.45        30.21 

  NUP93 MUTATED NUP93 WILD-TYPE 
           4.83            0.16 
  NUP93 MUTATED NUP93 WILD-TYPE 
          33.93          169.32 
  NUP93 MUTATED NUP93 WILD-TYPE 
         15.975          31.040 
[1] "4.8 - 33.9 (16.0)"  "0.2 - 169.3 (31.0)"
[1] "hr="     "1200000"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NUP93 MUTATED         2        0         2        0         0         0
  NUP93 WILD-TYPE     229       43        82        2        33         6
D5V3, multiclass
           clus
vv          NUP93 MUTATED NUP93 WILD-TYPE
  STAGE I               2             229
  STAGE II              0              43
  STAGE III             2              82
  STAGE IV              0               2
  STAGE IVA             0              33
  STAGE IVC             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUP93 MUTATED     2   1   1   0
  NUP93 WILD-TYPE 115 135 130  15
D5V4, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  T1             2             115
  T2             1             135
  T3             1             130
  T4             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                 cls
clus                0   1
  NUP93 MUTATED     1   3
  NUP93 WILD-TYPE 189 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      1    3
  NUP93 WILD-TYPE  189  167
   clus
vv  NUP93 MUTATED NUP93 WILD-TYPE
  0             1             189
  1             3             167
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   0
  NUP93 WILD-TYPE 219   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    0
  NUP93 WILD-TYPE  219    7
   clus
vv  NUP93 MUTATED NUP93 WILD-TYPE
  0             3             219
  1             0               7
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   1
  NUP93 WILD-TYPE 295 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  295  102
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  FEMALE             3             295
  MALE               1             102
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  NUP93 MUTATED     1   3
  NUP93 WILD-TYPE 160 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      1    3
  NUP93 WILD-TYPE  160  220
     clus
vv    NUP93 MUTATED NUP93 WILD-TYPE
  NO              1             160
  YES             3             220
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NUP93 MUTATED                1                                             1
  NUP93 WILD-TYPE              4                                           280
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NUP93 MUTATED                                                                        1
  NUP93 WILD-TYPE                                                                     84
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NUP93 MUTATED                                                                     1
  NUP93 WILD-TYPE                                                                  29
D5V9, multiclass
                                                                        clus
vv                                                                       NUP93 MUTATED
  OTHER  SPECIFY                                                                     1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      1
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                1
                                                                        clus
vv                                                                       NUP93 WILD-TYPE
  OTHER  SPECIFY                                                                       4
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      280
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   0
  NUP93 WILD-TYPE 333  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    0
  NUP93 WILD-TYPE  333   15
     clus
vv    NUP93 MUTATED NUP93 WILD-TYPE
  NO              3             333
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NUP93 MUTATED              1                       0    3                   0
  NUP93 WILD-TYPE          103                      11  269                   1
D5V11, multiclass
                         clus
vv                        NUP93 MUTATED NUP93 WILD-TYPE
  MINIMAL (T3)                        1             103
  MODERATE/ADVANCED (T4A)             0              11
  NONE                                3             269
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUP93 MUTATED     3   1   0   0
  NUP93 WILD-TYPE 311  36   3  22
D5V12, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  R0             3             311
  R1             1              36
  R2             0               3
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
D5V14, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   1
  NUP93 WILD-TYPE 178 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  178  210
            clus
vv           NUP93 MUTATED NUP93 WILD-TYPE
  MULTIFOCAL             3             178
  UNIFOCAL               1             210
[1] 2 2
[1] FALSE
D5V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP93 MUTATED       0                         1     2
  NUP93 WILD-TYPE    38                        17   263
D5V16, multiclass
                           clus
vv                          NUP93 MUTATED NUP93 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 2             263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V17, binary
                 cls
clus                0   1
  NUP93 MUTATED     0   3
  NUP93 WILD-TYPE  31 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      0    3
  NUP93 WILD-TYPE   31  288
                        clus
vv                       NUP93 MUTATED NUP93 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             3             288
[1] 2 2
[1] FALSE

Clustering(6) Variable = PPM1D MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  PPM1D MUTATED     4   0
  PPM1D WILD-TYPE 382  14
  PPM1D MUTATED PPM1D WILD-TYPE 
              4             396 
  PPM1D MUTATED PPM1D WILD-TYPE 
              0              14 
$`PPM1D MUTATED`
TCGA-DJ-A1QL TCGA-DJ-A2PW TCGA-E8-A418 TCGA-ET-A3BW 
       17.59        34.85         3.02        46.65 

$`PPM1D WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       51.39        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
       35.54        32.45        30.97        11.08        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       36.39        23.31        18.64        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
       12.66        12.30        12.79        12.46        10.68        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       18.54        18.84         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       33.96        31.99        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74         6.77        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX 
       36.33        32.81        36.33        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       35.87        23.21        24.82        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       36.43        24.76        17.23        27.62        30.87        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       27.06        26.93        35.54         3.12        15.81        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        92.55        47.21        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       80.52        63.19        52.44        39.95        31.23        35.67 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
       29.98        31.04        25.45         0.16        14.96         7.69 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
        0.39         0.39        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
      158.83         7.66        45.53        60.95       157.15        37.94 
TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 
       57.01       106.62         4.18        79.50       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       69.57        57.11       108.36        64.87        49.51        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX 
      115.10        65.39       136.01        50.37        50.20       147.75 
TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 
      101.13       139.99        49.32        33.50        43.36        49.71 
TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY 
       83.57       139.00       150.48       108.66        57.63        17.52 
TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       52.50        29.65       147.42       142.52       129.57        32.48 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
      132.07        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       82.82        78.97        51.78        53.06        61.22        60.16 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       30.51        53.36        44.15        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        13.64        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR 
       14.14        33.07        13.38         8.35        29.72        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM 
        0.49         9.24        13.91        38.66        21.34         5.33 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       26.37        22.45        21.53        24.46        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
       81.70        77.56        70.42        65.29        63.45        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       37.25        52.60        54.35         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       43.73        62.83       166.62        24.72        40.21        33.17 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC 
      117.40        66.77       112.80        81.83        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       16.14        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 
       18.08         0.76        17.06        15.16         1.35        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       17.00        21.67        12.46         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       47.41        18.51        16.90        17.23        43.17        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68        18.64        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         9.50        36.10        32.45        30.21 

  PPM1D MUTATED PPM1D WILD-TYPE 
           3.02            0.16 
  PPM1D MUTATED PPM1D WILD-TYPE 
          46.65          169.32 
  PPM1D MUTATED PPM1D WILD-TYPE 
          26.22           31.04 
[1] "3.0 - 46.6 (26.2)"  "0.2 - 169.3 (31.0)"
[1] "hr="     "3300000"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  PPM1D MUTATED         1        1         2        0         1         0
  PPM1D WILD-TYPE     230       42        82        2        32         6
D6V3, multiclass
           clus
vv          PPM1D MUTATED PPM1D WILD-TYPE
  STAGE I               1             230
  STAGE II              1              42
  STAGE III             2              82
  STAGE IV              0               2
  STAGE IVA             1              32
  STAGE IVC             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPM1D MUTATED     1   2   1   1
  PPM1D WILD-TYPE 116 134 130  14
D6V4, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  T1             1             116
  T2             2             134
  T3             1             130
  T4             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   2
  PPM1D WILD-TYPE 188 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    2
  PPM1D WILD-TYPE  188  168
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             2             188
  1             2             168
[1] 2 2
[1] FALSE
D6V6, binary
                 cls
clus                0   1
  PPM1D MUTATED     3   0
  PPM1D WILD-TYPE 219   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      3    0
  PPM1D WILD-TYPE  219    7
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             3             219
  1             0               7
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  PPM1D MUTATED     3   2
  PPM1D WILD-TYPE 295 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      3    2
  PPM1D WILD-TYPE  295  101
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  FEMALE             3             295
  MALE               2             101
[1] 2 2
[1] FALSE
D6V8, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   2
  PPM1D WILD-TYPE 159 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    2
  PPM1D WILD-TYPE  159  221
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              2             159
  YES             2             221
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  PPM1D MUTATED                0                                             4
  PPM1D WILD-TYPE              5                                           277
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  PPM1D MUTATED                                                                        1
  PPM1D WILD-TYPE                                                                     84
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  PPM1D MUTATED                                                                     0
  PPM1D WILD-TYPE                                                                  30
D6V9, multiclass
                                                                        clus
vv                                                                       PPM1D MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       PPM1D WILD-TYPE
  OTHER  SPECIFY                                                                       5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      277
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                 cls
clus                0   1
  PPM1D MUTATED     4   0
  PPM1D WILD-TYPE 332  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      4    0
  PPM1D WILD-TYPE  332   15
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              4             332
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  PPM1D MUTATED              0                       1    4                   0
  PPM1D WILD-TYPE          104                      10  268                   1
D6V11, multiclass
                         clus
vv                        PPM1D MUTATED PPM1D WILD-TYPE
  MINIMAL (T3)                        0             104
  MODERATE/ADVANCED (T4A)             1              10
  NONE                                4             268
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPM1D MUTATED     4   0   0   1
  PPM1D WILD-TYPE 310  37   3  21
D6V12, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  R0             4             310
  R1             0              37
  R2             0               3
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
[1] "Remove cluster labels:" "PPM1D MUTATED"         
clus
  PPM1D MUTATED PPM1D WILD-TYPE 
              2             303 
     TCGA-BJ-A0Z0      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A0ZB      TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A28R      TCGA-BJ-A28T 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A28X      TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A3EZ      TCGA-BJ-A3PR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A3PU      TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45G 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A3MD      TCGA-CE-A484 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-CE-A485      TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DJ-A13M      TCGA-DJ-A13O 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13R      TCGA-DJ-A13T      TCGA-DJ-A13V      TCGA-DJ-A13W 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13X      TCGA-DJ-A1QG      TCGA-DJ-A1QH      TCGA-DJ-A1QM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PO      TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PS      TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PX      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A3UK 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3UU      TCGA-DJ-A3UW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UX      TCGA-DJ-A3V7      TCGA-DJ-A3VA      TCGA-DJ-A3VB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VK      TCGA-DJ-A3VL 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UW      TCGA-DJ-A4V2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A4V5      TCGA-DO-A1K0      TCGA-DO-A2HM      TCGA-E3-A3DY 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A242      TCGA-E8-A2EA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A415      TCGA-E8-A419      TCGA-E8-A433      TCGA-E8-A436 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A44K      TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GQ      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GX      TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3T0      TCGA-EL-A3T1 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3T2      TCGA-EL-A3TB      TCGA-EL-A3ZH      TCGA-EL-A3ZK 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3ZN      TCGA-EL-A4JV      TCGA-EL-A4JW      TCGA-EL-A4JX 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2      TCGA-EL-A4K4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG      TCGA-EL-A4KI 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1CW      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K      TCGA-EM-A22L 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O      TCGA-EM-A22P 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN      TCGA-EM-A2CP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OX      TCGA-EM-A2OY      TCGA-EM-A2OZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2      TCGA-EM-A3AJ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AO 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3AQ      TCGA-EM-A3AR      TCGA-EM-A3FJ      TCGA-EM-A3FK 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FM      TCGA-EM-A3FN      TCGA-EM-A3FO      TCGA-EM-A3FP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FQ      TCGA-EM-A3FR      TCGA-EM-A3O3      TCGA-EM-A3O8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3O9      TCGA-EM-A3OA      TCGA-EM-A3OB      TCGA-EM-A4FM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A4FO      TCGA-EM-A4FQ      TCGA-EM-A4FR      TCGA-EM-A4FV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I      TCGA-ET-A25J 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A2MZ      TCGA-ET-A2N0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A2N1      TCGA-ET-A2N4      TCGA-ET-A39K      TCGA-ET-A39L 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39O      TCGA-ET-A39P      TCGA-ET-A39R      TCGA-ET-A39S 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BO      TCGA-ET-A3BP      TCGA-ET-A3BQ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BX      TCGA-ET-A3DQ      TCGA-ET-A3DR      TCGA-ET-A3DS 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV      TCGA-ET-A3DW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A3PB      TCGA-FE-A3PC      TCGA-FE-A3PD      TCGA-FK-A3S3 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FK-A3SB      TCGA-FK-A3SE      TCGA-FK-A3SG      TCGA-FK-A3SH 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3NM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7      TCGA-FY-A3R9 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3      TCGA-GE-A2C6 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH      TCGA-H2-A3RI 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED      TCGA-IM-A3U2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J      TCGA-KS-A4I5 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP      TCGA-L6-A4EU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
D6V14, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   3
  PPM1D WILD-TYPE 179 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    3
  PPM1D WILD-TYPE  179  208
            clus
vv           PPM1D MUTATED PPM1D WILD-TYPE
  MULTIFOCAL             2             179
  UNIFOCAL               3             208
[1] 2 2
[1] FALSE
D6V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPM1D MUTATED       0                         0     3
  PPM1D WILD-TYPE    38                        18   262
D6V16, multiclass
                           clus
vv                          PPM1D MUTATED PPM1D WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V17, binary
                 cls
clus                0   1
  PPM1D MUTATED     0   4
  PPM1D WILD-TYPE  31 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    4
  PPM1D WILD-TYPE   31  287
                        clus
vv                       PPM1D MUTATED PPM1D WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             4             287
[1] 2 2
[1] FALSE

Clustering(7) Variable = KRAS MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 382  14
  KRAS MUTATED KRAS WILD-TYPE 
             4            396 
  KRAS MUTATED KRAS WILD-TYPE 
             0             14 
$`KRAS MUTATED`
TCGA-BJ-A0ZE TCGA-EM-A2CQ TCGA-EM-A4FV TCGA-H2-A3RH 
       16.73        12.30        24.46        12.46 

$`KRAS WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        11.57        25.48        15.12        42.08        51.39 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       41.52         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        30.97        11.08        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64        10.88        21.01         3.45        23.84 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
       12.30        12.79        12.46        10.68        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.84         9.96        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        35.87        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       35.67        29.98        31.04         3.02        25.45         0.16 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 
      129.57        32.48       132.07        98.24        41.29       107.47 
TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN 
        5.72        66.90        82.82        78.97        51.78        53.06 
TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX 
       61.22        60.16        59.44        57.47        34.72        45.96 
TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD 
       37.94        31.04        30.51        53.36        44.15        43.59 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       24.30        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
       48.49        18.05        19.79        19.46        78.61        57.01 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M 
       54.08        14.73        14.50        15.75        10.45        14.53 
TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK 
       10.65        44.19        41.29        14.24        47.57        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CR TCGA-EM-A2CT 
       13.18        23.51         6.05         2.99        13.64        48.46 
TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ 
       13.15        22.16        40.34        19.73        32.32        33.96 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ 
       15.68        14.14        33.07        13.38         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       17.49        17.39        16.18        15.02        14.50        15.06 
TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK 
        7.33         0.49         9.24        13.91        38.66        21.34 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25G 
        5.33        26.37        22.45        21.53        13.68        81.93 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
       81.70        77.56        70.42        65.29        63.45        58.75 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       37.25        52.60        54.35         2.66        80.88        33.24 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
      106.09       107.41       108.46        84.89       123.32       100.57 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       95.34        94.13        55.10        98.20        28.24        50.40 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
       79.10        76.64         5.79        87.62        77.82        75.42 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
       46.65        52.47       116.78        94.59        84.85        80.58 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
       66.84        43.73        62.83       166.62        24.72        40.21 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       33.17        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB 
       68.22       117.40        66.77       112.80        81.83        85.15 
TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       85.68        78.77        71.08         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
        0.92        48.10         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        0.99        16.14        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 
       16.57        18.08         0.76        17.06        15.16         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       12.53        17.00        21.67         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       47.41        18.51        16.90        17.23        43.17        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68        18.64        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         9.50        36.10        32.45        30.21 

  KRAS MUTATED KRAS WILD-TYPE 
         12.30           0.16 
  KRAS MUTATED KRAS WILD-TYPE 
         24.46         169.32 
  KRAS MUTATED KRAS WILD-TYPE 
        14.595         31.135 
[1] "12.3 - 24.5 (14.6)" "0.2 - 169.3 (31.1)"
[1] "hr="     "1200000"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  KRAS MUTATED         3        0         1        0         0         0
  KRAS WILD-TYPE     228       43        83        2        33         6
D7V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              3            228
  STAGE II             0             43
  STAGE III            1             83
  STAGE IV             0              2
  STAGE IVA            0             33
  STAGE IVC            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED     3   0   1   0
  KRAS WILD-TYPE 114 136 130  15
D7V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            3            114
  T2            0            136
  T3            1            130
  T4            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                cls
clus               0   1
  KRAS MUTATED     3   1
  KRAS WILD-TYPE 187 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    1
  KRAS WILD-TYPE  187  169
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            3            187
  1            1            169
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus               0   1
  KRAS MUTATED     2   0
  KRAS WILD-TYPE 220   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    0
  KRAS WILD-TYPE  220    7
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            2            220
  1            0              7
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 294 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    0
  KRAS WILD-TYPE  294  103
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            4            294
  MALE              0            103
[1] 2 2
[1] FALSE
D7V8, binary
                cls
clus               0   1
  KRAS MUTATED     2   2
  KRAS WILD-TYPE 159 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    2
  KRAS WILD-TYPE  159  221
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             2            159
  YES            2            221
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  KRAS MUTATED                0                                             2
  KRAS WILD-TYPE              5                                           279
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  KRAS MUTATED                                                                        2
  KRAS WILD-TYPE                                                                     83
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  KRAS MUTATED                                                                     0
  KRAS WILD-TYPE                                                                  30
D7V9, multiclass
                                                                        clus
vv                                                                       KRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       KRAS WILD-TYPE
  OTHER  SPECIFY                                                                      5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             83
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                cls
clus               0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 332  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    0
  KRAS WILD-TYPE  332   15
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             4            332
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  KRAS MUTATED              1                       0    3                   0
  KRAS WILD-TYPE          103                      11  269                   1
D7V11, multiclass
                         clus
vv                        KRAS MUTATED KRAS WILD-TYPE
  MINIMAL (T3)                       1            103
  MODERATE/ADVANCED (T4A)            0             11
  NONE                               3            269
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED     2   1   0   0
  KRAS WILD-TYPE 312  36   3  22
D7V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0            2            312
  R1            1             36
  R2            0              3
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
D7V14, binary
                cls
clus               0   1
  KRAS MUTATED     2   2
  KRAS WILD-TYPE 179 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    2
  KRAS WILD-TYPE  179  209
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  MULTIFOCAL            2            179
  UNIFOCAL              2            209
[1] 2 2
[1] FALSE
D7V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     2
  KRAS WILD-TYPE    38                        18   263
D7V16, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            319 
    TCGA-BJ-A0YZ     TCGA-BJ-A0Z2     TCGA-BJ-A0Z3     TCGA-BJ-A0Z9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZA     TCGA-BJ-A0ZB     TCGA-BJ-A0ZC     TCGA-BJ-A0ZG 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A0ZH     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y     TCGA-BJ-A18Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A191     TCGA-BJ-A192     TCGA-BJ-A28R     TCGA-BJ-A28S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A28T     TCGA-BJ-A28V     TCGA-BJ-A28X     TCGA-BJ-A28Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A290     TCGA-BJ-A2N7     TCGA-BJ-A2N8     TCGA-BJ-A2N9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A2NA     TCGA-BJ-A2P4     TCGA-BJ-A3EZ     TCGA-BJ-A3F0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A3PR     TCGA-BJ-A3PT     TCGA-BJ-A3PU     TCGA-BJ-A45D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A45E     TCGA-BJ-A45F     TCGA-BJ-A45G     TCGA-BJ-A45I 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BJ-A45J     TCGA-BJ-A45K     TCGA-BJ-A4O8     TCGA-BJ-A4O9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A13K     TCGA-CE-A27D     TCGA-CE-A3MD     TCGA-CE-A3ME 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CE-A482     TCGA-CE-A484     TCGA-CE-A485     TCGA-DE-A0XZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A0Y2     TCGA-DE-A0Y3     TCGA-DE-A2OL     TCGA-DE-A3KN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DE-A4M8     TCGA-DE-A4M9     TCGA-DJ-A13L     TCGA-DJ-A13M 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13O     TCGA-DJ-A13P     TCGA-DJ-A13R     TCGA-DJ-A13S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A13T     TCGA-DJ-A13U     TCGA-DJ-A13W     TCGA-DJ-A1QD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QE     TCGA-DJ-A1QF     TCGA-DJ-A1QG     TCGA-DJ-A1QH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A1QI     TCGA-DJ-A1QM     TCGA-DJ-A1QO     TCGA-DJ-A1QQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PN     TCGA-DJ-A2PO     TCGA-DJ-A2PQ     TCGA-DJ-A2PR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PS     TCGA-DJ-A2PT     TCGA-DJ-A2PU     TCGA-DJ-A2PV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2PW     TCGA-DJ-A2PX     TCGA-DJ-A2PY     TCGA-DJ-A2PZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2     TCGA-DJ-A2Q3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q4     TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB     TCGA-DJ-A3UK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UM     TCGA-DJ-A3UN     TCGA-DJ-A3UO     TCGA-DJ-A3UQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UR     TCGA-DJ-A3US     TCGA-DJ-A3UT     TCGA-DJ-A3UU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3UW     TCGA-DJ-A3UX     TCGA-DJ-A3UY     TCGA-DJ-A3V7 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3VE     TCGA-DJ-A3VF     TCGA-DJ-A3VJ     TCGA-DJ-A3VK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3VL     TCGA-DJ-A3VM     TCGA-DJ-A4UL     TCGA-DJ-A4UP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A4UT     TCGA-DJ-A4UW     TCGA-DJ-A4V0     TCGA-DJ-A4V4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A4V5     TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-DO-A2HM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3DY     TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3E2     TCGA-E3-A3E3     TCGA-E3-A3E5     TCGA-E8-A242 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A2EA     TCGA-E8-A413     TCGA-E8-A415     TCGA-E8-A418 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A419     TCGA-E8-A433     TCGA-E8-A436     TCGA-E8-A437 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A44K     TCGA-E8-A44M     TCGA-EL-A3CL     TCGA-EL-A3CM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CN     TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CS     TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CW     TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D0     TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D6     TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GR     TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GW     TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H1     TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H5     TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3MX     TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3N3     TCGA-EL-A3T0     TCGA-EL-A3T1     TCGA-EL-A3T2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T3     TCGA-EL-A3T6     TCGA-EL-A3T7     TCGA-EL-A3T8 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T9     TCGA-EL-A3TA     TCGA-EL-A3TB     TCGA-EL-A3ZH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3ZK     TCGA-EL-A3ZN     TCGA-EL-A3ZQ     TCGA-EL-A3ZR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3ZT     TCGA-EL-A4JV     TCGA-EL-A4JW     TCGA-EL-A4JX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4JZ     TCGA-EL-A4K0     TCGA-EL-A4K2     TCGA-EL-A4K4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4K6     TCGA-EL-A4KD     TCGA-EL-A4KG     TCGA-EL-A4KH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4KI     TCGA-EM-A22M     TCGA-EM-A22O     TCGA-EM-A2OV 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A3AI     TCGA-ET-A25G     TCGA-ET-A25I     TCGA-ET-A25J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A25K     TCGA-ET-A25O     TCGA-ET-A25R     TCGA-ET-A2MY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2N5     TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39K 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39M     TCGA-ET-A39N     TCGA-ET-A39O     TCGA-ET-A39P 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39R     TCGA-ET-A39S     TCGA-ET-A39T     TCGA-ET-A3BN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BO     TCGA-ET-A3BP     TCGA-ET-A3BQ     TCGA-ET-A3BS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BX     TCGA-ET-A3DO     TCGA-ET-A3DP     TCGA-ET-A3DQ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DR     TCGA-ET-A3DS     TCGA-ET-A3DT     TCGA-ET-A3DU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-ET-A40S     TCGA-ET-A4KN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A22Z     TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A233     TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A237     TCGA-FE-A23A     TCGA-FE-A3PB     TCGA-FE-A3PC 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A3PD     TCGA-FK-A3S3     TCGA-FK-A3SB     TCGA-FK-A3SD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FK-A3SE     TCGA-FK-A3SG     TCGA-FK-A3SH     TCGA-FY-A2QD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3BL     TCGA-FY-A3I4     TCGA-FY-A3I5     TCGA-FY-A3NM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3NP     TCGA-FY-A3ON     TCGA-FY-A3R6     TCGA-FY-A3R7 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3R8     TCGA-FY-A3R9     TCGA-FY-A3RA     TCGA-FY-A3W9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3WA     TCGA-FY-A40K     TCGA-FY-A4B3     TCGA-GE-A2C6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-H2-A26U     TCGA-H2-A2K9     TCGA-H2-A3RI     TCGA-H2-A421 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IM-A3EB     TCGA-IM-A3ED     TCGA-IM-A3U2     TCGA-IM-A3U3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1     TCGA-J8-A3YE 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A4HW     TCGA-KS-A41J     TCGA-KS-A4I5     TCGA-KS-A4I9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KS-A4IB     TCGA-L6-A4EP     TCGA-L6-A4ET     TCGA-L6-A4EU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MK-A4N6     TCGA-MK-A4N7     TCGA-MK-A4N9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D7V17, binary
                cls
clus               0   1
  KRAS MUTATED     0   2
  KRAS WILD-TYPE  31 289
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    2
  KRAS WILD-TYPE   31  289
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            2            289
[1] 2 2
[1] FALSE

Clustering(8) Variable = DLC1 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 383  13
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            396 
  DLC1 MUTATED DLC1 WILD-TYPE 
             1             13 
$`DLC1 MUTATED`
TCGA-EL-A3CR TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EM-A2OW 
        7.66        29.65       132.07        40.34 

$`DLC1 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       51.39        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
       35.54        32.45        30.97        11.08        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       36.39        23.31        18.64        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
       12.66        12.30        12.79        12.46        10.68        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       18.54        18.84         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42        34.36        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        35.87        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       30.87        21.34        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 
       31.23        35.67        29.98        31.04         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
        0.16        14.96         7.69         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CS TCGA-EL-A3CT 
       26.73       155.54        97.74       158.83        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 
       57.63        17.52        52.50       147.42       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA 
       32.48        98.24        41.29       107.47         5.72        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       82.82        78.97        51.78        53.06        61.22        60.16 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       30.51        53.36        44.15        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        13.64        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       22.16        19.73        32.32        33.96        17.59        17.46 
TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL 
       17.29        14.60        22.52        30.94        15.68        14.14 
TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       33.07        13.38         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO 
        9.24        13.91        38.66        21.34         5.33        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       22.45        21.53        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       77.56        70.42        65.29        63.45        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       52.60        54.35         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       43.73        62.83       166.62        24.72        40.21        33.17 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC 
      117.40        66.77       112.80        81.83        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       16.14        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 
       18.08         0.76        17.06        15.16         1.35        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       17.00        21.67        12.46         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       47.41        18.51        16.90        17.23        43.17        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68        18.64        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         9.50        36.10        32.45        30.21 

  DLC1 MUTATED DLC1 WILD-TYPE 
          7.66           0.16 
  DLC1 MUTATED DLC1 WILD-TYPE 
        132.07         169.32 
  DLC1 MUTATED DLC1 WILD-TYPE 
        34.995         31.040 
[1] "7.7 - 132.1 (35.0)" "0.2 - 169.3 (31.0)"
[1] "hr=" "6.4"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  DLC1 MUTATED         2        1         1        0         0         0
  DLC1 WILD-TYPE     229       42        83        2        33         6
D8V3, multiclass
           clus
vv          DLC1 MUTATED DLC1 WILD-TYPE
  STAGE I              2            229
  STAGE II             1             42
  STAGE III            1             83
  STAGE IV             0              2
  STAGE IVA            0             33
  STAGE IVC            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLC1 MUTATED     1   2   1   0
  DLC1 WILD-TYPE 116 134 130  15
D8V4, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  T1            1            116
  T2            2            134
  T3            1            130
  T4            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                cls
clus               0   1
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE 189 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE  189  168
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            1            189
  1            2            168
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus               0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 219   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    0
  DLC1 WILD-TYPE  219    7
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            3            219
  1            0              7
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 295 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    1
  DLC1 WILD-TYPE  295  102
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  FEMALE            3            295
  MALE              1            102
[1] 2 2
[1] FALSE
D8V8, binary
                cls
clus               0   1
  DLC1 MUTATED     2   2
  DLC1 WILD-TYPE 159 221
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      2    2
  DLC1 WILD-TYPE  159  221
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             2            159
  YES            2            221
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DLC1 MUTATED                0                                             3
  DLC1 WILD-TYPE              5                                           278
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DLC1 MUTATED                                                                        1
  DLC1 WILD-TYPE                                                                     84
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DLC1 MUTATED                                                                     0
  DLC1 WILD-TYPE                                                                  30
D8V9, multiclass
                                                                        clus
vv                                                                       DLC1 MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     3
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)            1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       DLC1 WILD-TYPE
  OTHER  SPECIFY                                                                      5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                cls
clus               0   1
  DLC1 MUTATED     4   0
  DLC1 WILD-TYPE 332  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      4    0
  DLC1 WILD-TYPE  332   15
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             4            332
  YES            0             15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  DLC1 MUTATED              2                       0    2                   0
  DLC1 WILD-TYPE          102                      11  270                   1
D8V11, multiclass
                         clus
vv                        DLC1 MUTATED DLC1 WILD-TYPE
  MINIMAL (T3)                       2            102
  MODERATE/ADVANCED (T4A)            0             11
  NONE                               2            270
  VERY ADVANCED (T4B)                0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DLC1 MUTATED     3   1   0   0
  DLC1 WILD-TYPE 311  36   3  22
D8V12, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  R0            3            311
  R1            1             36
  R2            0              3
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2            303 
    TCGA-BJ-A0Z0     TCGA-BJ-A0Z3     TCGA-BJ-A0Z9     TCGA-BJ-A0ZA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A0ZB     TCGA-BJ-A0ZH     TCGA-BJ-A0ZJ     TCGA-BJ-A18Y 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A18Z     TCGA-BJ-A191     TCGA-BJ-A28R     TCGA-BJ-A28T 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A28X     TCGA-BJ-A28Z     TCGA-BJ-A290     TCGA-BJ-A2N8 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A2N9     TCGA-BJ-A2NA     TCGA-BJ-A3EZ     TCGA-BJ-A3PR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A3PU     TCGA-BJ-A45D     TCGA-BJ-A45E     TCGA-BJ-A45G 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A45I     TCGA-BJ-A45J     TCGA-BJ-A45K     TCGA-BJ-A4O8 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-BJ-A4O9     TCGA-CE-A13K     TCGA-CE-A3MD     TCGA-CE-A484 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-CE-A485     TCGA-DE-A0XZ     TCGA-DE-A0Y2     TCGA-DE-A0Y3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DE-A3KN     TCGA-DE-A4M8     TCGA-DJ-A13M     TCGA-DJ-A13O 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13R     TCGA-DJ-A13T     TCGA-DJ-A13V     TCGA-DJ-A13W 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13X     TCGA-DJ-A1QG     TCGA-DJ-A1QH     TCGA-DJ-A1QM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PO     TCGA-DJ-A2PP     TCGA-DJ-A2PQ     TCGA-DJ-A2PR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PS     TCGA-DJ-A2PT     TCGA-DJ-A2PU     TCGA-DJ-A2PV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PW     TCGA-DJ-A2PX     TCGA-DJ-A2PY     TCGA-DJ-A2PZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q0     TCGA-DJ-A2Q1     TCGA-DJ-A2Q2     TCGA-DJ-A2Q3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q4     TCGA-DJ-A2Q5     TCGA-DJ-A2Q6     TCGA-DJ-A2Q7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q8     TCGA-DJ-A2Q9     TCGA-DJ-A2QA     TCGA-DJ-A2QB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3UK     TCGA-DJ-A3UM     TCGA-DJ-A3UN     TCGA-DJ-A3UO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3UP     TCGA-DJ-A3UQ     TCGA-DJ-A3UR     TCGA-DJ-A3UU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3UW     TCGA-DJ-A3UX     TCGA-DJ-A3V7     TCGA-DJ-A3VA 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3VB     TCGA-DJ-A3VF     TCGA-DJ-A3VJ     TCGA-DJ-A3VK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3VL     TCGA-DJ-A4UL     TCGA-DJ-A4UP     TCGA-DJ-A4UW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A4V2     TCGA-DJ-A4V5     TCGA-DO-A1K0     TCGA-DO-A2HM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3DY     TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3E2     TCGA-E3-A3E3     TCGA-E3-A3E5     TCGA-E8-A242 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E8-A2EA     TCGA-E8-A415     TCGA-E8-A419     TCGA-E8-A433 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E8-A436     TCGA-E8-A44K     TCGA-EL-A3CM     TCGA-EL-A3CN 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CO     TCGA-EL-A3CS     TCGA-EL-A3CT     TCGA-EL-A3CU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CV     TCGA-EL-A3CW     TCGA-EL-A3CX     TCGA-EL-A3CY 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CZ     TCGA-EL-A3D0     TCGA-EL-A3D1     TCGA-EL-A3D4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3D5     TCGA-EL-A3D6     TCGA-EL-A3GO     TCGA-EL-A3GP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GQ     TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3MZ     TCGA-EL-A3T0     TCGA-EL-A3T1     TCGA-EL-A3T2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3TB     TCGA-EL-A3ZH     TCGA-EL-A3ZK     TCGA-EL-A3ZN 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A4JV     TCGA-EL-A4JW     TCGA-EL-A4JX     TCGA-EL-A4JZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A4K0     TCGA-EL-A4K2     TCGA-EL-A4K4     TCGA-EL-A4K6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A4KD     TCGA-EL-A4KG     TCGA-EL-A4KI     TCGA-EM-A1CS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1CT     TCGA-EM-A1CU     TCGA-EM-A1CV     TCGA-EM-A1CW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1YC     TCGA-EM-A1YD     TCGA-EM-A1YE     TCGA-EM-A22I 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22J     TCGA-EM-A22K     TCGA-EM-A22L     TCGA-EM-A22M 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22N     TCGA-EM-A22O     TCGA-EM-A22P     TCGA-EM-A22Q 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CK     TCGA-EM-A2CN     TCGA-EM-A2CP     TCGA-EM-A2CQ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CR     TCGA-EM-A2CT     TCGA-EM-A2CU     TCGA-EM-A2OV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2OX     TCGA-EM-A2OY     TCGA-EM-A2OZ     TCGA-EM-A2P0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2P1     TCGA-EM-A2P2     TCGA-EM-A3AJ     TCGA-EM-A3AK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO     TCGA-EM-A3AQ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AR     TCGA-EM-A3FJ     TCGA-EM-A3FK     TCGA-EM-A3FM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FN     TCGA-EM-A3FO     TCGA-EM-A3FP     TCGA-EM-A3FQ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FR     TCGA-EM-A3O3     TCGA-EM-A3O8     TCGA-EM-A3O9 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3OA     TCGA-EM-A3OB     TCGA-EM-A4FM     TCGA-EM-A4FO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A4FQ     TCGA-EM-A4FR     TCGA-EM-A4FV     TCGA-EM-A4G1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A25G     TCGA-ET-A25I     TCGA-ET-A25J     TCGA-ET-A25K 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A25O     TCGA-ET-A2MZ     TCGA-ET-A2N0     TCGA-ET-A2N1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2N4     TCGA-ET-A39K     TCGA-ET-A39L     TCGA-ET-A39O 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39P     TCGA-ET-A39R     TCGA-ET-A39S     TCGA-ET-A39T 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BO     TCGA-ET-A3BP     TCGA-ET-A3BQ     TCGA-ET-A3BS 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BT     TCGA-ET-A3BU     TCGA-ET-A3BV     TCGA-ET-A3BX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DQ     TCGA-ET-A3DR     TCGA-ET-A3DS     TCGA-ET-A3DT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DU     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-ET-A40S 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A4KN     TCGA-FE-A22Z     TCGA-FE-A230     TCGA-FE-A231 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A232     TCGA-FE-A233     TCGA-FE-A234     TCGA-FE-A235 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A236     TCGA-FE-A237     TCGA-FE-A23A     TCGA-FE-A3PB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A3PC     TCGA-FE-A3PD     TCGA-FK-A3S3     TCGA-FK-A3SB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FK-A3SE     TCGA-FK-A3SG     TCGA-FK-A3SH     TCGA-FY-A2QD 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A3I4     TCGA-FY-A3I5     TCGA-FY-A3NM     TCGA-FY-A3NN 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A3ON     TCGA-FY-A3R6     TCGA-FY-A3R7     TCGA-FY-A3R9 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A3W9     TCGA-FY-A40K     TCGA-FY-A4B3     TCGA-GE-A2C6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-H2-A26U     TCGA-H2-A2K9     TCGA-H2-A3RH     TCGA-H2-A3RI 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-H2-A421     TCGA-IM-A3EB     TCGA-IM-A3ED     TCGA-IM-A3U2 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-IM-A3U3     TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-J8-A3YE     TCGA-J8-A4HW     TCGA-KS-A41J     TCGA-KS-A4I5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-KS-A4I9     TCGA-KS-A4IB     TCGA-L6-A4EP     TCGA-L6-A4EU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-MK-A4N6     TCGA-MK-A4N7     TCGA-MK-A4N9 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
D8V14, binary
                cls
clus               0   1
  DLC1 MUTATED     1   3
  DLC1 WILD-TYPE 180 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    3
  DLC1 WILD-TYPE  180  208
            clus
vv           DLC1 MUTATED DLC1 WILD-TYPE
  MULTIFOCAL            1            180
  UNIFOCAL              3            208
[1] 2 2
[1] FALSE
D8V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED       0                         0     3
  DLC1 WILD-TYPE    38                        18   262
D8V16, multiclass
                           clus
vv                          DLC1 MUTATED DLC1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                3            262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V17, binary
                cls
clus               0   1
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE  30 289
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE   30  289
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO            2            289
[1] 2 2
[1] FALSE

Clustering(9) Variable = ITGAL MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  ITGAL MUTATED     3   1
  ITGAL WILD-TYPE 383  13
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             396 
  ITGAL MUTATED ITGAL WILD-TYPE 
              1              13 
$`ITGAL MUTATED`
TCGA-BJ-A0ZB TCGA-EL-A3T3 TCGA-EL-A3T9 TCGA-EM-A3AO 
        4.01       132.07         5.72        13.38 

$`ITGAL WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73        25.48        15.12        42.08        51.39 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       41.52         4.83        44.35        42.15        21.04        35.54 
TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 
       32.45        30.97        11.08        30.21        18.38        16.57 
TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 TCGA-BJ-A3PR 
       20.48        18.97         7.04        16.01        13.94        36.39 
TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F TCGA-BJ-A45G 
       23.31        18.64        10.88        21.01         3.45        23.84 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
       12.30        12.79        12.46        10.68        12.43        12.66 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       35.84        21.63        50.17        37.64        15.85        18.54 
TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R 
       18.84         9.96        48.79        38.17       169.32        18.58 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        43.17        52.37         8.32 
TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI 
       11.01       135.91        30.61        44.98        42.51        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       17.59         6.02        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT 
        7.82        30.58        35.41        27.45        26.20        38.83 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
       33.96        31.99        34.85        28.96         8.78         8.42 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
       34.36        37.74         6.77        40.24        33.93        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        35.11        39.09        35.90        33.53        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        36.92        31.04        32.42        31.46        16.41 
TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW 
       19.56        36.33        32.81        36.33        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        35.87        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
        7.76        36.43        24.76        17.23        27.62        30.87 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        27.06        26.93        35.54         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       35.38        54.90        21.53         2.33        92.55        47.21 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        80.52        63.19        52.44        39.95        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       35.67        29.98        31.04         3.02        25.45         0.16 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69         0.39         0.39        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT 
      155.54        97.74       158.83         7.66        45.53        60.95 
TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ 
      157.15        37.94        57.01       106.62         4.18        79.50 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        69.57        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
       49.51        50.24       115.10        65.39       136.01        50.37 
TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.20       147.75       101.13       139.99        49.32        33.50 
TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
       43.36        49.71        83.57       139.00       150.48       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 
       57.63        17.52        52.50        29.65       147.42       142.52 
TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA 
      129.57        32.48        98.24        41.29       107.47        66.90 
TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       82.82        78.97        51.78        53.06        61.22        60.16 
TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 
       59.44        57.47        34.72        45.96        37.94        31.04 
TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH 
       30.51        53.36        44.15        43.59        24.30        27.06 
TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW 
       23.90        26.86        18.18        20.91        48.49        18.05 
TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I 
       19.79        19.46        78.61        57.01        54.08        14.73 
TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O 
       14.50        15.75        10.45        14.53        10.65        44.19 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       41.29        14.24        47.57        17.88        13.18        23.51 
TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU 
        6.05         2.99        12.30        13.64        48.46        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        40.34        19.73        32.32        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK 
       17.46        17.29        14.60        22.52        30.94        15.68 
TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ 
       14.14        33.07         8.35        29.72        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP 
       23.77        47.38        21.01        12.07        17.49        17.39 
TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 
       16.18        15.02        14.50        15.06         7.33         0.49 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO 
        9.24        13.91        38.66        21.34         5.33        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       22.45        21.53        24.46        13.68        81.93        81.70 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       77.56        70.42        65.29        63.45        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       52.60        54.35         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       94.13        55.10        98.20        28.24        50.40        79.10 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
       76.64         5.79        87.62        77.82        75.42        46.65 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
       52.47       116.78        94.59        84.85        80.58        66.84 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       43.73        62.83       166.62        24.72        40.21        33.17 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        71.44        31.59        79.69        24.69        68.22 
TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC 
      117.40        66.77       112.80        81.83        85.15        85.68 
TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       78.77        71.08         4.11         1.05        13.28         0.92 
TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM 
       48.10         1.25        20.42        17.82         7.82         0.99 
TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 
       16.14        19.56        13.91        16.27        15.68        16.57 
TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 
       18.08         0.76        17.06        15.16         1.35        12.53 
TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       17.00        21.67        12.46         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 
       47.41        18.51        16.90        17.23        43.17        27.19 
TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB 
       27.85         2.60        15.68        18.64        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83         9.50        36.10        32.45        30.21 

  ITGAL MUTATED ITGAL WILD-TYPE 
           4.01            0.16 
  ITGAL MUTATED ITGAL WILD-TYPE 
         132.07          169.32 
  ITGAL MUTATED ITGAL WILD-TYPE 
           9.55           31.04 
[1] "4.0 - 132.1 (9.6)"  "0.2 - 169.3 (31.0)"
[1] "hr=" "8.5"
D9V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  ITGAL MUTATED         0        1         0        1         2         0
  ITGAL WILD-TYPE     231       42        84        1        31         6
D9V3, multiclass
           clus
vv          ITGAL MUTATED ITGAL WILD-TYPE
  STAGE I               0             231
  STAGE II              1              42
  STAGE III             0              84
  STAGE IV              1               1
  STAGE IVA             2              31
  STAGE IVC             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAL MUTATED     0   2   1   1
  ITGAL WILD-TYPE 117 134 130  14
D9V4, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  T1             0             117
  T2             2             134
  T3             1             130
  T4             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 189 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  189  167
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0             1             189
  1             3             167
[1] 2 2
[1] FALSE
D9V6, binary
                 cls
clus                0   1
  ITGAL MUTATED     2   0
  ITGAL WILD-TYPE 220   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      2    0
  ITGAL WILD-TYPE  220    7
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0             2             220
  1             0               7
[1] 2 2
[1] FALSE
D9V7, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 297 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  297  100
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  FEMALE             1             297
  MALE               3             100
[1] 2 2
[1] FALSE
D9V8, binary
                 cls
clus                0   1
  ITGAL MUTATED     0   3
  ITGAL WILD-TYPE 161 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      0    3
  ITGAL WILD-TYPE  161  220
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO              0             161
  YES             3             220
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  ITGAL MUTATED                0                                             4
  ITGAL WILD-TYPE              5                                           277
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  ITGAL MUTATED                                                                        0
  ITGAL WILD-TYPE                                                                     85
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  ITGAL MUTATED                                                                     0
  ITGAL WILD-TYPE                                                                  30
D9V9, multiclass
                                                                        clus
vv                                                                       ITGAL MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       ITGAL WILD-TYPE
  OTHER  SPECIFY                                                                       5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      277
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              85
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                 cls
clus                0   1
  ITGAL MUTATED     4   0
  ITGAL WILD-TYPE 332  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      4    0
  ITGAL WILD-TYPE  332   15
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO              4             332
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  ITGAL MUTATED              0                       1    2                   1
  ITGAL WILD-TYPE          104                      10  270                   0
D9V11, multiclass
                         clus
vv                        ITGAL MUTATED ITGAL WILD-TYPE
  MINIMAL (T3)                        0             104
  MODERATE/ADVANCED (T4A)             1              10
  NONE                                2             270
  VERY ADVANCED (T4B)                 1               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGAL MUTATED     2   2   0   0
  ITGAL WILD-TYPE 312  35   3  22
D9V12, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  R0             2             312
  R1             2              35
  R2             0               3
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2             303 
     TCGA-BJ-A0Z0      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A28R      TCGA-BJ-A28T      TCGA-BJ-A28X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N8      TCGA-BJ-A2N9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A2NA      TCGA-BJ-A3EZ      TCGA-BJ-A3PR      TCGA-BJ-A3PU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45G      TCGA-BJ-A45I 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8      TCGA-BJ-A4O9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-CE-A13K      TCGA-CE-A3MD      TCGA-CE-A484      TCGA-CE-A485 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A3KN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A4M8      TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13T      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QG      TCGA-DJ-A1QH      TCGA-DJ-A1QM      TCGA-DJ-A2PO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PX      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB      TCGA-DJ-A3UK 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3UU      TCGA-DJ-A3UW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UX      TCGA-DJ-A3V7      TCGA-DJ-A3VA      TCGA-DJ-A3VB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VK      TCGA-DJ-A3VL 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UW      TCGA-DJ-A4V2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A4V5      TCGA-DO-A1K0      TCGA-DO-A2HM      TCGA-E3-A3DY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A242      TCGA-E8-A2EA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A415      TCGA-E8-A419      TCGA-E8-A433      TCGA-E8-A436 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A44K      TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GQ      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GX      TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3T0      TCGA-EL-A3T1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3T2      TCGA-EL-A3TB      TCGA-EL-A3ZH      TCGA-EL-A3ZK 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3ZN      TCGA-EL-A4JV      TCGA-EL-A4JW      TCGA-EL-A4JX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2      TCGA-EL-A4K4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG      TCGA-EL-A4KI 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CW      TCGA-EM-A1YC      TCGA-EM-A1YD      TCGA-EM-A1YE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K      TCGA-EM-A22L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O      TCGA-EM-A22P 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN      TCGA-EM-A2CP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A2OX      TCGA-EM-A2OY      TCGA-EM-A2OZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2      TCGA-EM-A3AJ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AR      TCGA-EM-A3FJ      TCGA-EM-A3FK      TCGA-EM-A3FM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FN      TCGA-EM-A3FO      TCGA-EM-A3FP      TCGA-EM-A3FQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FR      TCGA-EM-A3O3      TCGA-EM-A3O8      TCGA-EM-A3O9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3OA      TCGA-EM-A3OB      TCGA-EM-A4FM      TCGA-EM-A4FO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A4FQ      TCGA-EM-A4FR      TCGA-EM-A4FV      TCGA-EM-A4G1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A25G      TCGA-ET-A25I      TCGA-ET-A25J      TCGA-ET-A25K 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A25O      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2N4      TCGA-ET-A39K      TCGA-ET-A39L      TCGA-ET-A39O 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39P      TCGA-ET-A39R      TCGA-ET-A39S      TCGA-ET-A39T 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BO      TCGA-ET-A3BP      TCGA-ET-A3BQ      TCGA-ET-A3BS 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DQ      TCGA-ET-A3DR      TCGA-ET-A3DS      TCGA-ET-A3DT 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DU      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-ET-A40S 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A231 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A      TCGA-FE-A3PB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A3PC      TCGA-FE-A3PD      TCGA-FK-A3S3      TCGA-FK-A3SB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FK-A3SE      TCGA-FK-A3SG      TCGA-FK-A3SH      TCGA-FY-A2QD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3NM      TCGA-FY-A3NN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7      TCGA-FY-A3R9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3      TCGA-GE-A2C6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH      TCGA-H2-A3RI 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED      TCGA-IM-A3U2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J      TCGA-KS-A4I5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP      TCGA-L6-A4EU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
D9V14, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 180 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  180  208
            clus
vv           ITGAL MUTATED ITGAL WILD-TYPE
  MULTIFOCAL             1             180
  UNIFOCAL               3             208
[1] 2 2
[1] FALSE
D9V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGAL MUTATED       0                         0     3
  ITGAL WILD-TYPE    38                        18   262
D9V16, multiclass
                           clus
vv                          ITGAL MUTATED ITGAL WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V17, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   2
  ITGAL WILD-TYPE  30 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    2
  ITGAL WILD-TYPE   30  289
                        clus
vv                       ITGAL MUTATED ITGAL WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO             2             289
[1] 2 2
[1] FALSE

Clustering(10) Variable = TG MUTATION ANALYSIS
D10V1, survival
              sevent
clus2            0   1
  TG MUTATED    10   1
  TG WILD-TYPE 376  13
  TG MUTATED TG WILD-TYPE 
          11          389 
  TG MUTATED TG WILD-TYPE 
           1           13 
$`TG MUTATED`
TCGA-BJ-A45F TCGA-CE-A3MD TCGA-DE-A2OL TCGA-DJ-A2PP TCGA-EL-A3H1 TCGA-EL-A3ZQ 
        3.45        12.79        37.64        30.58        49.32        61.22 
TCGA-EM-A3AI TCGA-EM-A3AO TCGA-EM-A3FR TCGA-ET-A25I TCGA-ET-A3BO 
       22.52        13.38        15.02        81.70        50.40 

$`TG WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       51.39        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
       35.54        32.45        30.97        11.08        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45G 
       36.39        23.31        18.64        10.88        21.01        23.84 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
       15.45        21.63        23.18        19.43        23.47        12.66 
TCGA-CE-A27D TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ 
       12.30        12.46        10.68        12.43        12.66        35.84 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L 
       21.63        50.17        15.85        18.54        18.84         9.96 
TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T 
       48.79        38.17       169.32        18.58         8.71        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
       23.38        43.17        52.37         8.32        11.01       135.91 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM 
       30.61        44.98        42.51        14.96        17.59         6.02 
TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PQ 
       42.58        47.41        17.56        10.09         7.82        35.41 
TCGA-DJ-A2PR TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW 
       27.45        26.20        38.83        33.96        31.99        34.85 
TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 
       28.96         8.78         8.42        34.36        37.74         6.77 
TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 
       40.24        33.93        37.48        36.46        35.11        39.09 
TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM 
       35.90        33.53        35.18        15.88        36.92        31.04 
TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       32.42        31.46        16.41        19.56        36.33        32.81 
TCGA-DJ-A3UT TCGA-DJ-A3UU TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 
       36.33        17.69        59.57        11.34        35.87        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK 
       24.82        22.92        18.97         7.76        36.43        24.76 
TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW 
       17.23        27.62        30.87        21.34        27.06        26.93 
TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 
       35.54         3.12        15.81        35.38        54.90        21.53 
TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 
        2.33        92.55        47.21        66.38        80.52        63.19 
TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 
       52.44        39.95        31.23        35.67        29.98        31.04 
TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
        3.02        25.45         0.16        14.96         7.69         0.39 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
        0.39        31.66        26.73       155.54        97.74       158.83 
TCGA-EL-A3CR TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW 
        7.66        45.53        60.95       157.15        37.94        57.01 
TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 
      106.62         4.18        79.50       139.86        98.53        69.57 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87        49.51        50.24       115.10 
TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY 
       65.39       136.01        50.37        50.20       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        33.50        43.36        49.71        83.57       139.00 
TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 
      150.48       108.66        57.63        17.52        52.50        29.65 
TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 
      147.42       142.52       129.57        32.48       132.07        98.24 
TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH 
       41.29       107.47         5.72        66.90        82.82        78.97 
TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       51.78        53.06        60.16        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        53.36        44.15 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AP TCGA-EM-A3AQ 
       30.94        15.68        14.14        33.07         8.35        29.72 
TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN 
       37.25        27.95        23.77        47.38        21.01        12.07 
TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.49        17.39        16.18        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM 
        0.49         9.24        13.91        38.66        21.34         5.33 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G 
       26.37        22.45        21.53        24.46        13.68        81.93 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       77.56        70.42        65.29        63.45        58.75        37.25 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       52.60        54.35         2.66        80.88        33.24       106.09 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
      107.41       108.46        84.89       123.32       100.57        95.34 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ 
       94.13        55.10        98.20        28.24        79.10        76.64 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.79        87.62        77.82        75.42        46.65        52.47 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
      116.78        94.59        84.85        80.58        66.84        43.73 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       62.83       166.62        24.72        40.21        33.17        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       71.44        31.59        79.69        24.69        68.22       117.40 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD 
       66.77       112.80        81.83        85.15        85.68        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH 
       71.08         4.11         1.05        13.28         0.92        48.10 
TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP 
        1.25        20.42        17.82         7.82         0.99        16.14 
TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA 
       19.56        13.91        16.27        15.68        16.57        18.08 
TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U 
        0.76        17.06        15.16         1.35        12.53        17.00 
TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED 
       21.67        12.46         2.99        20.05        48.92        47.41 
TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE 
       18.51        16.90        17.23        43.17        27.19        27.85 
TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP 
        2.60        15.68        18.64        87.39        84.72        33.40 
TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       21.83         9.50        36.10        32.45        30.21 

  TG MUTATED TG WILD-TYPE 
        3.45         0.16 
  TG MUTATED TG WILD-TYPE 
       81.70       169.32 
  TG MUTATED TG WILD-TYPE 
       30.58        31.04 
[1] "3.5 - 81.7 (30.6)"  "0.2 - 169.3 (31.0)"
[1] "hr=" "3.1"
D10V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  TG MUTATED         6        3         1        0         1         0
  TG WILD-TYPE     225       40        83        2        32         6
D10V3, multiclass
           clus
vv          TG MUTATED TG WILD-TYPE
  STAGE I            6          225
  STAGE II           3           40
  STAGE III          1           83
  STAGE IV           0            2
  STAGE IVA          1           32
  STAGE IVC          0            6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  TG MUTATED     2   8   1   0
  TG WILD-TYPE 115 128 130  15
D10V4, multiclass
    clus
vv   TG MUTATED TG WILD-TYPE
  T1          2          115
  T2          8          128
  T3          1          130
  T4          0           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
              cls
clus             0   1
  TG MUTATED     5   4
  TG WILD-TYPE 185 166
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      5    4
  TG WILD-TYPE  185  166
   clus
vv  TG MUTATED TG WILD-TYPE
  0          5          185
  1          4          166
[1] 2 2
[1] FALSE
D10V6, binary
              cls
clus             0   1
  TG MUTATED     5   0
  TG WILD-TYPE 217   7
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      5    0
  TG WILD-TYPE  217    7
   clus
vv  TG MUTATED TG WILD-TYPE
  0          5          217
  1          0            7
[1] 2 2
[1] FALSE
D10V7, binary
              cls
clus             0   1
  TG MUTATED     8   3
  TG WILD-TYPE 290 100
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      8    3
  TG WILD-TYPE  290  100
        clus
vv       TG MUTATED TG WILD-TYPE
  FEMALE          8          290
  MALE            3          100
[1] 2 2
[1] FALSE
D10V8, binary
              cls
clus             0   1
  TG MUTATED     3   8
  TG WILD-TYPE 158 215
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      3    8
  TG WILD-TYPE  158  215
     clus
vv    TG MUTATED TG WILD-TYPE
  NO           3          158
  YES          8          215
[1] 2 2
[1] FALSE
              vv
clus           OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  TG MUTATED                0                                             6
  TG WILD-TYPE              5                                           275
              vv
clus           THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  TG MUTATED                                                                        4
  TG WILD-TYPE                                                                     81
              vv
clus           THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  TG MUTATED                                                                     1
  TG WILD-TYPE                                                                  29
D10V9, multiclass
                                                                        clus
vv                                                                       TG MUTATED
  OTHER  SPECIFY                                                                  0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   6
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)          4
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)             1
                                                                        clus
vv                                                                       TG WILD-TYPE
  OTHER  SPECIFY                                                                    5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   275
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           81
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
              cls
clus             0   1
  TG MUTATED     8   0
  TG WILD-TYPE 328  15
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      8    0
  TG WILD-TYPE  328   15
     clus
vv    TG MUTATED TG WILD-TYPE
  NO           8          328
  YES          0           15
[1] 2 2
[1] FALSE
              vv
clus           MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  TG MUTATED              1                       0    9                   0
  TG WILD-TYPE          103                      11  263                   1
D10V11, multiclass
                         clus
vv                        TG MUTATED TG WILD-TYPE
  MINIMAL (T3)                     1          103
  MODERATE/ADVANCED (T4A)          0           11
  NONE                             9          263
  VERY ADVANCED (T4B)              0            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  TG MUTATED     9   1   0   0
  TG WILD-TYPE 305  36   3  22
D10V12, multiclass
    clus
vv   TG MUTATED TG WILD-TYPE
  R0          9          305
  R1          1           36
  R2          0            3
  RX          0           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
D10V14, binary
              cls
clus             0   1
  TG MUTATED     5   6
  TG WILD-TYPE 176 205
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      5    6
  TG WILD-TYPE  176  205
            clus
vv           TG MUTATED TG WILD-TYPE
  MULTIFOCAL          5          176
  UNIFOCAL            6          205
[1] 2 2
[1] FALSE
D10V15, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TG MUTATED       1                         1     6
  TG WILD-TYPE    37                        17   259
D10V16, multiclass
                           clus
vv                          TG MUTATED TG WILD-TYPE
  ASIAN                              1           37
  BLACK OR AFRICAN AMERICAN          1           17
  WHITE                              6          259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V17, binary
              cls
clus             0   1
  TG MUTATED     0   9
  TG WILD-TYPE  31 282
[1] "tbl2"
              cls
clus           [,1] [,2]
  TG MUTATED      0    9
  TG WILD-TYPE   31  282
                        clus
vv                       TG MUTATED TG WILD-TYPE
  HISPANIC OR LATINO              0           31
  NOT HISPANIC OR LATINO          9          282
[1] 2 2
[1] FALSE

Clustering(11) Variable = NLRP6 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  NLRP6 MUTATED     3   0
  NLRP6 WILD-TYPE 383  14
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             397 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              0              14 
$`NLRP6 MUTATED`
TCGA-EM-A3FO TCGA-FE-A3PC TCGA-FK-A3S3 
       17.49        85.68        71.08 

$`NLRP6 WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ 
        4.01        11.57        16.73        25.48        15.12        42.08 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       51.39        41.52         4.83        44.35        42.15        21.04 
TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 
       35.54        32.45        30.97        11.08        30.21        18.38 
TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2NA TCGA-BJ-A2P4 TCGA-BJ-A3EZ TCGA-BJ-A3F0 
       16.57        20.48        18.97         7.04        16.01        13.94 
TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E TCGA-BJ-A45F 
       36.39        23.31        18.64        10.88        21.01         3.45 
TCGA-BJ-A45G TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       23.84        15.45        21.63        23.18        19.43        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
       12.66        12.30        12.79        12.46        10.68        12.43 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.66        35.84        21.63        50.17        37.64        15.85 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       18.54        18.84         9.96        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        23.38        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        11.01       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96        17.59         6.02        42.58        47.41        17.56 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
       10.09         7.82        30.58        35.41        27.45        26.20 
TCGA-DJ-A2PT TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY 
       38.83        33.96        31.99        34.85        28.96         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 
        8.42        34.36        37.74         6.77        40.24        33.93 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        35.11        39.09        35.90        33.53 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        36.92        31.04        32.42        31.46 
TCGA-DJ-A3UP TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UU 
       16.41        19.56        36.33        32.81        36.33        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        35.87        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VK TCGA-DJ-A3VL TCGA-DJ-A3VM 
       18.97         7.76        36.43        24.76        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       30.87        21.34        27.06        26.93        35.54         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        35.38        54.90        21.53         2.33        92.55 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       47.21        66.38        80.52        63.19        52.44        39.95 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 
       31.23        35.67        29.98        31.04         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
        0.16        14.96         7.69         0.39         0.39        31.66 
TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CR TCGA-EL-A3CS 
       26.73       155.54        97.74       158.83         7.66        45.53 
TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CY 
       60.95       157.15        37.94        57.01       106.62         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       79.50       139.86        98.53        69.57        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87        49.51        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GW TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 
       50.37        50.20       147.75       101.13       139.99        49.32 
TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 
       33.50        43.36        49.71        83.57       139.00       150.48 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 
      108.66        57.63        17.52        52.50        29.65       147.42 
TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 
      142.52       129.57        32.48       132.07        98.24        41.29 
TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZH TCGA-EL-A3ZK 
      107.47         5.72        66.90        82.82        78.97        51.78 
TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT TCGA-EL-A4JV TCGA-EL-A4JW 
       53.06        61.22        60.16        59.44        57.47        34.72 
TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 
       45.96        37.94        31.04        30.51        53.36        44.15 
TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT 
       43.59        24.30        27.06        23.90        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        48.49        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L 
       57.01        54.08        14.73        14.50        15.75        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        44.19        41.29        14.24        47.57 
TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ 
       17.88        13.18        23.51         6.05         2.99        12.30 
TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
       13.64        48.46        13.15        22.16        40.34        19.73 
TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 
       32.32        33.96        17.59        17.46        17.29        14.60 
TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO 
       22.52        30.94        15.68        14.14        33.07        13.38 
TCGA-EM-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL 
        8.35        29.72        37.25        27.95        23.77        47.38 
TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       21.01        12.07        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB 
       15.06         7.33         0.49         9.24        13.91        38.66 
TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV 
       21.34         5.33        26.37        22.45        21.53        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
       13.68        81.93        81.70        77.56        70.42        65.29 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       63.45        58.75        37.25        52.60        54.35         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       80.88        33.24       106.09       107.41       108.46        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
      123.32       100.57        95.34        94.13        55.10        98.20 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24        50.40        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       77.82        75.42        46.65        52.47       116.78        94.59 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       84.85        80.58        66.84        43.73        62.83       166.62 
TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       24.72        40.21        33.17        73.74        71.44        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       79.69        24.69        68.22       117.40        66.77       112.80 
TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PD TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE 
       81.83        85.15        78.77         4.11         1.05        13.28 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 
        0.92        48.10         1.25        20.42        17.82         7.82 
TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 TCGA-FY-A3R8 
        0.99        16.14        19.56        13.91        16.27        15.68 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 
       16.57        18.08         0.76        17.06        15.16         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 
       12.53        17.00        21.67        12.46         2.99        20.05 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O0 
       48.92        47.41        18.51        16.90        17.23        43.17 
TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 
       27.19        27.85         2.60        15.68        18.64        87.39 
TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU TCGA-MK-A4N6 TCGA-MK-A4N7 
       84.72        33.40        21.83         9.50        36.10        32.45 
TCGA-MK-A4N9 
       30.21 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
          17.49            0.16 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          85.68          169.32 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          71.08           31.04 
[1] "17.5 - 85.7 (71.1)" "0.2 - 169.3 (31.0)"
[1] "hr="     "9100000"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  NLRP6 MUTATED         3        0         0        0         0         0
  NLRP6 WILD-TYPE     228       43        84        2        33         6
D11V3, multiclass
           clus
vv          NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I               3             228
  STAGE II              0              43
  STAGE III             0              84
  STAGE IV              0               2
  STAGE IVA             0              33
  STAGE IVC             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRP6 MUTATED     0   0   3   0
  NLRP6 WILD-TYPE 117 136 128  15
D11V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             0             117
  T2             0             136
  T3             3             128
  T4             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                 cls
clus                0   1
  NLRP6 MUTATED     1   2
  NLRP6 WILD-TYPE 189 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE  189  168
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1             189
  1             2             168
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   0
  NLRP6 WILD-TYPE 222   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    0
  NLRP6 WILD-TYPE  222    7
D11V7, binary
                 cls
clus                0   1
  NLRP6 MUTATED     2   1
  NLRP6 WILD-TYPE 296 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  296  102
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             2             296
  MALE               1             102
[1] 2 2
[1] FALSE
D11V8, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   3
  NLRP6 WILD-TYPE 161 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    3
  NLRP6 WILD-TYPE  161  220
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              0             161
  YES             3             220
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NLRP6 MUTATED                0                                             2
  NLRP6 WILD-TYPE              5                                           279
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NLRP6 MUTATED                                                                        1
  NLRP6 WILD-TYPE                                                                     84
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NLRP6 MUTATED                                                                     0
  NLRP6 WILD-TYPE                                                                  30
D11V9, multiclass
                                                                        clus
vv                                                                       NLRP6 MUTATED
  OTHER  SPECIFY                                                                     0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      2
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             1
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                0
                                                                        clus
vv                                                                       NLRP6 WILD-TYPE
  OTHER  SPECIFY                                                                       5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              84
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                 cls
clus                0   1
  NLRP6 MUTATED     3   0
  NLRP6 WILD-TYPE 333  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      3    0
  NLRP6 WILD-TYPE  333   15
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              3             333
  YES             0              15
[1] 2 2
[1] FALSE
                 vv
clus              MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  NLRP6 MUTATED              1                       0    2                   0
  NLRP6 WILD-TYPE          103                      11  270                   1
D11V11, multiclass
                         clus
vv                        NLRP6 MUTATED NLRP6 WILD-TYPE
  MINIMAL (T3)                        1             103
  MODERATE/ADVANCED (T4A)             0              11
  NONE                                2             270
  VERY ADVANCED (T4B)                 0               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NLRP6 MUTATED     3   0   0   0
  NLRP6 WILD-TYPE 311  37   3  22
D11V12, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             3             311
  R1             0              37
  R2             0               3
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
D11V14, binary
                 cls
clus                0   1
  NLRP6 MUTATED     2   1
  NLRP6 WILD-TYPE 179 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  179  210
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  MULTIFOCAL             2             179
  UNIFOCAL               1             210
[1] 2 2
[1] FALSE
D11V15, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             325 
     TCGA-BJ-A0Z2      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9      TCGA-BJ-A0ZA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZB      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE      TCGA-BJ-A0ZG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y      TCGA-BJ-A18Z 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R      TCGA-BJ-A28S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28Z      TCGA-BJ-A290 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2N8      TCGA-BJ-A2N9      TCGA-BJ-A2P4      TCGA-BJ-A3PU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45F      TCGA-BJ-A45G 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A27D      TCGA-CE-A3MD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A3ME      TCGA-CE-A482      TCGA-CE-A484      TCGA-CE-A485 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A2OL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DE-A4M9      TCGA-DJ-A13L 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R      TCGA-DJ-A13S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13U      TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QH      TCGA-DJ-A1QI      TCGA-DJ-A1QL      TCGA-DJ-A1QM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QN      TCGA-DJ-A1QO      TCGA-DJ-A1QQ      TCGA-DJ-A2PN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PO      TCGA-DJ-A2PP      TCGA-DJ-A2PQ      TCGA-DJ-A2PR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PS      TCGA-DJ-A2PT      TCGA-DJ-A2PU      TCGA-DJ-A2PV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PW      TCGA-DJ-A2PY      TCGA-DJ-A2PZ      TCGA-DJ-A2Q0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q1      TCGA-DJ-A2Q2      TCGA-DJ-A2Q3      TCGA-DJ-A2Q4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q5      TCGA-DJ-A2Q6      TCGA-DJ-A2Q7      TCGA-DJ-A2Q8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QC      TCGA-DJ-A3UK 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO      TCGA-DJ-A3UP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3US      TCGA-DJ-A3UT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UU      TCGA-DJ-A3UW      TCGA-DJ-A3UX      TCGA-DJ-A3UY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3V7      TCGA-DJ-A3VA      TCGA-DJ-A3VB      TCGA-DJ-A3VE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VF      TCGA-DJ-A3VJ      TCGA-DJ-A3VK      TCGA-DJ-A3VL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VM      TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V0      TCGA-DJ-A4V2      TCGA-DJ-A4V4      TCGA-DJ-A4V5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-DO-A2HM      TCGA-E3-A3DY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E3      TCGA-E8-A419      TCGA-EL-A3CN      TCGA-EL-A3CO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GZ      TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N3      TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3T3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T6      TCGA-EL-A3T7      TCGA-EL-A3T8      TCGA-EL-A3T9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3TA      TCGA-EL-A3TB      TCGA-EL-A3ZH      TCGA-EL-A3ZK 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZN      TCGA-EL-A3ZQ      TCGA-EL-A3ZR      TCGA-EL-A3ZT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JV      TCGA-EL-A4JW      TCGA-EL-A4JX      TCGA-EL-A4JZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K0      TCGA-EL-A4K2      TCGA-EL-A4K4      TCGA-EL-A4K6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KD      TCGA-EL-A4KG      TCGA-EL-A4KH      TCGA-EL-A4KI 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CW      TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YD      TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22K      TCGA-EM-A22L      TCGA-EM-A22N      TCGA-EM-A22O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22P      TCGA-EM-A22Q      TCGA-EM-A2CJ      TCGA-EM-A2CK 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CL      TCGA-EM-A2CN      TCGA-EM-A2CO      TCGA-EM-A2CP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2OW      TCGA-EM-A2OX      TCGA-EM-A2OY      TCGA-EM-A2P0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2P1      TCGA-EM-A2P2      TCGA-EM-A2P3      TCGA-EM-A3AI 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AO      TCGA-EM-A3AP      TCGA-EM-A3AQ      TCGA-EM-A3AR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FJ      TCGA-EM-A3FM      TCGA-EM-A3FN      TCGA-EM-A3FP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FR      TCGA-EM-A3O3      TCGA-EM-A3O6      TCGA-EM-A3O7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3O8      TCGA-EM-A3O9      TCGA-EM-A3OA      TCGA-EM-A3OB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A4FK      TCGA-EM-A4FM      TCGA-EM-A4FQ      TCGA-EM-A4FR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A4FV      TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A25R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39J      TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39P      TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BP      TCGA-ET-A3BQ      TCGA-ET-A3BS      TCGA-ET-A3BT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BW      TCGA-ET-A3BX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DO      TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A40S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A232 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A237      TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3ON 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3R8      TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-GE-A2C6      TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3O0      TCGA-KS-A41J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-L6-A4ET      TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED       0                         1     1
  NLRP6 WILD-TYPE    38                        17   264
D11V16, multiclass
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             319 
     TCGA-BJ-A0YZ      TCGA-BJ-A0Z2      TCGA-BJ-A0Z3      TCGA-BJ-A0Z9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZA      TCGA-BJ-A0ZB      TCGA-BJ-A0ZC      TCGA-BJ-A0ZE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A0ZG      TCGA-BJ-A0ZH      TCGA-BJ-A0ZJ      TCGA-BJ-A18Y 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A18Z      TCGA-BJ-A191      TCGA-BJ-A192      TCGA-BJ-A28R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28S      TCGA-BJ-A28T      TCGA-BJ-A28V      TCGA-BJ-A28X 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A28Z      TCGA-BJ-A290      TCGA-BJ-A2N7      TCGA-BJ-A2N8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A2N9      TCGA-BJ-A2NA      TCGA-BJ-A2P4      TCGA-BJ-A3EZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A3F0      TCGA-BJ-A3PR      TCGA-BJ-A3PT      TCGA-BJ-A3PU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45D      TCGA-BJ-A45E      TCGA-BJ-A45F      TCGA-BJ-A45G 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A45I      TCGA-BJ-A45J      TCGA-BJ-A45K      TCGA-BJ-A4O8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-BJ-A4O9      TCGA-CE-A13K      TCGA-CE-A27D      TCGA-CE-A3MD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-CE-A3ME      TCGA-CE-A482      TCGA-CE-A484      TCGA-CE-A485 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A0XZ      TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A2OL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DE-A4M9      TCGA-DJ-A13L 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13P      TCGA-DJ-A13R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A13S      TCGA-DJ-A13T      TCGA-DJ-A13U      TCGA-DJ-A13W 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QD      TCGA-DJ-A1QE      TCGA-DJ-A1QF      TCGA-DJ-A1QG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QH      TCGA-DJ-A1QI      TCGA-DJ-A1QM      TCGA-DJ-A1QO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A1QQ      TCGA-DJ-A2PN      TCGA-DJ-A2PO      TCGA-DJ-A2PQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PT      TCGA-DJ-A2PU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PX      TCGA-DJ-A2PY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q3      TCGA-DJ-A2Q4      TCGA-DJ-A2Q5      TCGA-DJ-A2Q6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A2Q7      TCGA-DJ-A2Q9      TCGA-DJ-A2QA      TCGA-DJ-A2QB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UK      TCGA-DJ-A3UM      TCGA-DJ-A3UN      TCGA-DJ-A3UO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UQ      TCGA-DJ-A3UR      TCGA-DJ-A3US      TCGA-DJ-A3UT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3UU      TCGA-DJ-A3UW      TCGA-DJ-A3UX      TCGA-DJ-A3UY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3V7      TCGA-DJ-A3VE      TCGA-DJ-A3VF      TCGA-DJ-A3VJ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A3VK      TCGA-DJ-A3VL      TCGA-DJ-A3VM      TCGA-DJ-A4UL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4UP      TCGA-DJ-A4UT      TCGA-DJ-A4UW      TCGA-DJ-A4V0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V4      TCGA-DJ-A4V5      TCGA-DO-A1JZ      TCGA-DO-A1K0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DO-A2HM      TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E1      TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A242      TCGA-E8-A2EA      TCGA-E8-A413      TCGA-E8-A415 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A418      TCGA-E8-A419      TCGA-E8-A433      TCGA-E8-A436 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A437      TCGA-E8-A44K      TCGA-E8-A44M      TCGA-EL-A3CL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CM      TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GQ      TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GV      TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GZ      TCGA-EL-A3H1      TCGA-EL-A3H2      TCGA-EL-A3H3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H4      TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MW      TCGA-EL-A3MX      TCGA-EL-A3MY      TCGA-EL-A3MZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3N2      TCGA-EL-A3N3      TCGA-EL-A3T0      TCGA-EL-A3T1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T2      TCGA-EL-A3T3      TCGA-EL-A3T6      TCGA-EL-A3T7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T8      TCGA-EL-A3T9      TCGA-EL-A3TA      TCGA-EL-A3TB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZH      TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A3ZQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZR      TCGA-EL-A3ZT      TCGA-EL-A4JV      TCGA-EL-A4JW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KH      TCGA-EL-A4KI      TCGA-EM-A22M      TCGA-EM-A22O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2OV      TCGA-EM-A3AI      TCGA-ET-A25G      TCGA-ET-A25I 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A25R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MY      TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N4      TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39K      TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39O 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39P      TCGA-ET-A39R      TCGA-ET-A39S      TCGA-ET-A39T 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BN      TCGA-ET-A3BO      TCGA-ET-A3BP      TCGA-ET-A3BQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU      TCGA-ET-A3BV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BW      TCGA-ET-A3BX      TCGA-ET-A3DO      TCGA-ET-A3DP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DQ      TCGA-ET-A3DR      TCGA-ET-A3DS      TCGA-ET-A3DT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DU      TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-ET-A40S 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A231 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A      TCGA-FE-A3PB 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A3PD      TCGA-FK-A3SB      TCGA-FK-A3SD      TCGA-FK-A3SE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FK-A3SG      TCGA-FK-A3SH      TCGA-FY-A2QD      TCGA-FY-A3BL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3NM      TCGA-FY-A3NP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7      TCGA-FY-A3R8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3R9      TCGA-FY-A3RA      TCGA-FY-A3W9      TCGA-FY-A3WA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A40K      TCGA-FY-A4B3      TCGA-GE-A2C6      TCGA-H2-A26U 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H2-A2K9      TCGA-H2-A3RH      TCGA-H2-A3RI      TCGA-H2-A421 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3EB      TCGA-IM-A3ED      TCGA-IM-A3U2      TCGA-IM-A3U3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1      TCGA-J8-A3YE 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-J8-A4HW      TCGA-KS-A41J      TCGA-KS-A4I5      TCGA-KS-A4I9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A4IB      TCGA-L6-A4EP      TCGA-L6-A4ET      TCGA-L6-A4EU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
D11V17, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   2
  NLRP6 WILD-TYPE  31 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    2
  NLRP6 WILD-TYPE   31  289
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             2             289
[1] 2 2
[1] FALSE
