[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/15092795/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/15165022/transformed.cor.cli.txt"

nPatients in clinical file=501, in cluster file=401, common to both=400
[1] "Reduce the number of clustering variables from 12 to 11."
[1]  11 400
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           239            161 
  BRAF MUTATED BRAF WILD-TYPE 
           239            161 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            34            366 
  NRAS MUTATED NRAS WILD-TYPE 
            34            366 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14            386 
  HRAS MUTATED HRAS WILD-TYPE 
            14            386 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              394 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              394 
[1] "NUP93 MUTATION ANALYSIS"
[1] 3
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             396 
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             396 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             395 
  PPM1D MUTATED PPM1D WILD-TYPE 
              5             395 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              397 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              397 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             4            396 
  KRAS MUTATED KRAS WILD-TYPE 
             4            396 
[1] "DLC1 MUTATION ANALYSIS"
[1] 3
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            396 
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            396 
[1] "ITGAL MUTATION ANALYSIS"
[1] 3
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             396 
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             396 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             397 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             397 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "RADIATION_EXPOSURE"                    
[17] "EXTRATHYROIDAL_EXTENSION"              
[18] "COMPLETENESS_OF_RESECTION"             
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "MULTIFOCALITY"                         
[21] "TUMOR_SIZE"                            
[22] "RACE"                                  
[23] "ETHNICITY"                             
[24] "BATCH_NUMBER"                          

Input Data has 24 rows and 400 columns.

[1] "Batch" "24"   
[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=13,	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=351,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_SIZE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'BATCH_NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 400 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RADIATION_EXPOSURE"                    
[10] "EXTRATHYROIDAL_EXTENSION"              
[11] "COMPLETENESS_OF_RESECTION"             
[12] "NUMBER_OF_LYMPH_NODES"                 
[13] "MULTIFOCALITY"                         
[14] "TUMOR_SIZE"                            
[15] "RACE"                                  
[16] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=71, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
117 137 129  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
117 137 129  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
117 137 129  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
117 137 129  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
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=28, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=67, 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   229   9
  BRAF WILD-TYPE 157   4
  BRAF MUTATED BRAF WILD-TYPE 
           238            161 
  BRAF MUTATED BRAF WILD-TYPE 
             9              4 
$`BRAF MUTATED`
TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A18Z TCGA-BJ-A28R 
       16.34         8.25         4.01        15.12        20.71        42.15 
TCGA-BJ-A28S TCGA-BJ-A28X TCGA-BJ-A290 TCGA-BJ-A2NA TCGA-BJ-A3EZ TCGA-BJ-A3PR 
       21.04        17.52        30.21        18.97        16.01        15.48 
TCGA-BJ-A3PU TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A3ME 
       18.64         6.18        21.63         4.93        23.47         0.23 
TCGA-DE-A0XZ TCGA-DE-A0Y3 TCGA-DJ-A13L TCGA-DJ-A13O TCGA-DJ-A13P TCGA-DJ-A13T 
       20.22        36.46         9.96        14.07       169.32        56.19 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF 
       23.38        18.35         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 
        7.99        14.96         1.45        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         7.99        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 
       12.56         8.28        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 
        9.44        37.48        36.46        10.09        35.90        12.43 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ 
       15.88        15.09        31.04        20.45        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        21.37        23.21 
TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL 
       24.82        22.92        18.97         7.76        24.20        17.23 
TCGA-DJ-A4UL TCGA-DJ-A4UW TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DO-A1K0 TCGA-DO-A2HM 
       18.21        14.70         3.12        15.81        21.53         2.33 
TCGA-E3-A3DY TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       31.07        40.21        63.19        30.31        14.04        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       22.29        13.61        13.81         3.02        25.45        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
       14.96         7.69        13.78        31.66        26.73       155.54 
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-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D6 TCGA-EL-A3GP TCGA-EL-A3GQ 
       57.01       139.86        98.53       108.36         1.41        50.24 
TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY 
      115.10        65.39       136.01        50.37       147.75       101.13 
TCGA-EL-A3GZ TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW 
      139.99        49.71        83.57       139.00       131.15       108.66 
TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T1 
       57.63        17.52        52.50        29.65       147.42       129.57 
TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3ZQ 
      132.07        98.24        41.29       107.47        66.90        61.22 
TCGA-EL-A3ZT TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K4 
       59.44        34.72        45.96        37.94        31.04        53.36 
TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A22I 
       24.30        27.06        18.18        20.91        12.36        14.73 
TCGA-EM-A22M TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2OX TCGA-EM-A2OZ TCGA-EM-A2P0 
       14.53        11.74        11.15        19.73        33.96        17.59 
TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AK TCGA-EM-A3AR TCGA-EM-A3FJ 
       17.46        17.29        14.60        15.68        37.25        27.95 
TCGA-EM-A3FK TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3O3 TCGA-EM-A3O7 TCGA-EM-A3O8 
       23.77        21.01        17.49        14.50         7.33        12.53 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J 
        5.33        26.37        22.45        24.46        47.47        29.69 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       32.35        27.09        29.49        22.09        12.26        16.08 
TCGA-ET-A2N4 TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39M TCGA-ET-A39O TCGA-ET-A39P 
        2.66        71.01        80.02        84.89        61.02        58.72 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       55.10        59.15         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 
       69.24        17.98        25.32        24.72        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        24.69        68.22       117.40        66.77 
TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FK-A3SB TCGA-FK-A3SH 
       81.34        81.83        85.15        85.68         4.11        48.10 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3ON TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3RA 
       20.42        17.82        19.56        16.27        15.68        18.08 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RI TCGA-H2-A421 
       15.16         1.35        12.53        17.00         2.99        20.05 
TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3YE 
       48.92        47.41        10.26        16.90        17.23        27.85 
TCGA-KS-A41J TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET 
       15.68         6.74        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 

$`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        18.21        18.87        11.57        16.73 
TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28T 
        7.56        17.69        23.34         4.83        44.35        35.54 
TCGA-BJ-A28V TCGA-BJ-A28Z TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 
        5.10         1.22        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         6.35 
TCGA-BJ-A45K TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A482 TCGA-CE-A484 
        8.98         0.53         0.10         0.20        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 
        0.10        15.42         5.98        15.85        18.54        18.84 
TCGA-DJ-A13M TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13W TCGA-DJ-A1QG TCGA-DJ-A1QL 
       17.26         3.39         8.71        14.60        13.12         7.20 
TCGA-DJ-A2PP TCGA-DJ-A2PX TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q8 
        5.33         5.52        34.36        37.74         6.77         7.10 
TCGA-DJ-A2QB TCGA-DJ-A3UP TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3VM TCGA-DJ-A4UP 
       35.18        16.41        32.81        24.23        27.62        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4V0 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-E3-A3DZ TCGA-E3-A3E0 
       14.14        17.82        24.33        54.90        12.07        66.38 
TCGA-E8-A44M TCGA-EL-A3CO TCGA-EL-A3CX TCGA-EL-A3CY TCGA-EL-A3CZ TCGA-EL-A3D4 
       13.58        97.74        80.91         4.18        58.82        45.40 
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 
      130.72        32.48         5.72        82.82        78.97        31.50 
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        16.44        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        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OY TCGA-EM-A3AI TCGA-EM-A3AJ TCGA-EM-A3AL TCGA-EM-A3AN 
       13.84        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        16.80        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         7.82 
TCGA-EM-A4FK TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25I TCGA-ET-A2N1 TCGA-ET-A2N5 
       21.34        21.53        13.68        48.20        29.19        58.22 
TCGA-ET-A39I TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39R TCGA-ET-A3BN TCGA-ET-A3DQ 
       13.74        65.36        98.56        57.11        28.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A3PD 
       43.50         0.30       132.36         5.03         4.01        78.77 
TCGA-FK-A3S3 TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FY-A2QD TCGA-FY-A3I5 
       71.08         1.05        22.03         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 
          0.23           0.10 
  BRAF MUTATED BRAF WILD-TYPE 
        169.32         132.36 
  BRAF MUTATED BRAF WILD-TYPE 
         24.25          17.26 
[1] "0.2 - 169.3 (24.2)" "0.1 - 132.4 (17.3)"
[1] "hr=" "1"  
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  BRAF MUTATED       131       19        59        0        25         4
  BRAF WILD-TYPE      99       26        24        2         7         2
D1V3, multiclass
           clus
vv          BRAF MUTATED BRAF WILD-TYPE
  STAGE I            131             99
  STAGE II            19             26
  STAGE III           59             24
  STAGE IV             0              2
  STAGE IVA           25              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 67 89 13
  BRAF WILD-TYPE 48 70 40  2
D1V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           69             48
  T2           67             70
  T3           89             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    99 119
  BRAF WILD-TYPE  90  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     99  119
  BRAF WILD-TYPE   90   51
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           99             90
  1          119             51
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus               0   1
  BRAF MUTATED   141   5
  BRAF WILD-TYPE  80   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    141    5
  BRAF WILD-TYPE   80    2
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0          141             80
  1            5              2
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  BRAF MUTATED   173  66
  BRAF WILD-TYPE 125  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    173   66
  BRAF WILD-TYPE  125   36
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE          173            125
  MALE             66             36
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  BRAF MUTATED                3                                           193
  BRAF WILD-TYPE              3                                            88
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  BRAF MUTATED                                                                       15
  BRAF WILD-TYPE                                                                     68
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  BRAF MUTATED                                                                    28
  BRAF WILD-TYPE                                                                   2
D1V8, multiclass
                                                                        clus
vv                                                                       BRAF MUTATED
  OTHER  SPECIFY                                                                    3
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   193
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           15
  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"
D1V9, binary
                cls
clus               0   1
  BRAF MUTATED    11 228
  BRAF WILD-TYPE   1 160
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11  228
  BRAF WILD-TYPE    1  160
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            11              1
  YES          228            160
[1] 2 2
[1] FALSE
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             80                      11  143                   0
  BRAF WILD-TYPE           23                       0  129                   1
D1V11, multiclass
                         clus
vv                        BRAF MUTATED BRAF WILD-TYPE
  MINIMAL (T3)                      80             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   184  25   3  15
  BRAF WILD-TYPE 129  12   0   7
D1V12, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0          184            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   109 127
  BRAF WILD-TYPE  72  83
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED    109  127
  BRAF WILD-TYPE   72   83
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  MULTIFOCAL          109             72
  UNIFOCAL            127             83
[1] 2 2
[1] FALSE
D1V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED      24                        11   170
  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                              170             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    22 183
  BRAF WILD-TYPE   9 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     22  183
  BRAF WILD-TYPE    9  107
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO               22              9
  NOT HISPANIC OR LATINO          183            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  13
  NRAS MUTATED NRAS WILD-TYPE 
            34            365 
  NRAS MUTATED NRAS WILD-TYPE 
             0             13 
$`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         6.35 
TCGA-DJ-A13S TCGA-DJ-A1QG TCGA-DJ-A2PP TCGA-DJ-A3UP TCGA-DJ-A3UT TCGA-EL-A3GW 
        8.71        13.12         5.33        16.41        24.23        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        10.49         8.35 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4G1 TCGA-ET-A25I TCGA-FY-A3NP 
       13.91         7.82        21.34        13.68        48.20        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        18.21        16.34         8.25         4.01 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         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 
        5.10        17.52         1.22        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        15.48        18.64        10.88 
TCGA-BJ-A45E TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 
       21.01         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        3.39        56.19        23.38        18.35        14.60         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         7.99        14.96         7.20 
TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN TCGA-DJ-A2PO 
        1.45        42.58        47.41        17.56        10.09         7.99 
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        12.56         8.28 
TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 
       34.85         5.52         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         9.44        37.48        36.46        10.09 
TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK 
        7.10        35.90        12.43        35.18        15.88        15.09 
TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UQ TCGA-DJ-A3UR TCGA-DJ-A3US 
       31.04        20.45        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        21.37        23.21        24.82 
TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM 
       22.92        18.97         7.76        24.20        17.23        27.62 
TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 
       18.21        21.34        14.14        14.70        17.82         3.12 
TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY 
       15.81        24.33        54.90        21.53         2.33        31.07 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
       12.07        66.38        40.21        63.19        30.31        14.04 
TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 
       31.23        22.29        13.61        13.81         3.02        25.45 
TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL 
       14.70        14.96         7.69        13.78        13.58        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        80.91         4.18 
TCGA-EL-A3CZ TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 
       58.82       139.86        98.53        45.40        57.11       108.36 
TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU 
       64.87         1.41        50.24       115.10        65.39       136.01 
TCGA-EL-A3GV TCGA-EL-A3GX TCGA-EL-A3GY TCGA-EL-A3GZ TCGA-EL-A3H1 TCGA-EL-A3H2 
       50.37       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       131.15       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       130.72 
TCGA-EL-A3T1 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
      129.57       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR 
       66.90        82.82        31.50        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-A4K4 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EM-A1CS TCGA-EM-A1CT 
       53.36        43.59        24.30        27.06        26.86        18.18 
TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC 
       20.91        12.36        18.05        19.79        19.46        78.61 
TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22K TCGA-EM-A22M TCGA-EM-A22N 
       57.01        54.08        14.73        15.75        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CO 
       11.74        11.15        16.44        17.88        13.18         6.05 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX 
        2.99        12.30        13.15        22.16        13.84        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-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        17.39        16.18        15.02        14.50 
TCGA-EM-A3O6 TCGA-EM-A3O7 TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A4FM TCGA-EM-A4FO 
       15.06         7.33        12.53         9.24         5.33        26.37 
TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-ET-A25G TCGA-ET-A25J TCGA-ET-A25K 
       22.45        21.53        24.46        47.47        29.69        32.35 
TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 
       27.09        29.49        22.09        12.26        16.08        29.19 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        58.22        13.74        71.01        80.02        65.36 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89        98.56        61.02        58.72        57.11        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS 
       59.15        28.24         5.85         4.18         2.43         5.56 
TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO 
       24.72        38.30        42.25         2.37         4.50        80.81 
TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU 
       69.24        59.87        43.50         0.30        17.98        25.32 
TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 
      132.36        24.72         5.03         4.01        73.74        59.70 
TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 
       31.59        44.25        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 
       81.34        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        22.03         0.92        48.10         1.25 
TCGA-FY-A3BL TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3ON TCGA-FY-A3R6 
       20.42        17.82         7.82         0.99        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3RA TCGA-FY-A3WA TCGA-FY-A40K TCGA-FY-A4B3 
       16.27        15.68        18.08        17.06        15.16         1.35 
TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A3RH TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB 
       12.53        17.00        12.46         2.99        20.05        48.92 
TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ TCGA-J8-A3O1 TCGA-J8-A3YE 
       47.41        10.26        16.90        17.23        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         6.74        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 

  NRAS MUTATED NRAS WILD-TYPE 
          0.76           0.10 
  NRAS MUTATED NRAS WILD-TYPE 
         78.97         169.32 
  NRAS MUTATED NRAS WILD-TYPE 
         16.49          21.53 
[1] "0.8 - 79.0 (16.5)"  "0.1 - 169.3 (21.5)"
[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     208       39        79        1        32         5
D2V3, multiclass
           clus
vv          NRAS MUTATED NRAS WILD-TYPE
  STAGE I             22            208
  STAGE II             6             39
  STAGE III            4             79
  STAGE IV             1              1
  STAGE IVA            0             32
  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 107 120 123  14
D2V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1           10            107
  T2           17            120
  T3            6            123
  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 162 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     27    5
  NRAS WILD-TYPE  162  165
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           27            162
  1            5            165
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  NRAS MUTATED    17   1
  NRAS WILD-TYPE 204   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     17    1
  NRAS WILD-TYPE  204    6
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           17            204
  1            1              6
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  NRAS MUTATED    25   9
  NRAS WILD-TYPE 273  93
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     25    9
  NRAS WILD-TYPE  273   93
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           25            273
  MALE              9             93
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NRAS MUTATED                0                                            15
  NRAS WILD-TYPE              6                                           266
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NRAS MUTATED                                                                       19
  NRAS WILD-TYPE                                                                     64
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NRAS MUTATED                                                                     0
  NRAS WILD-TYPE                                                                  30
D2V8, multiclass
                                                                        clus
vv                                                                       NRAS MUTATED
  OTHER  SPECIFY                                                                    0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                    15
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)           19
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)               0
                                                                        clus
vv                                                                       NRAS WILD-TYPE
  OTHER  SPECIFY                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     266
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             64
  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"
D2V9, binary
                cls
clus               0   1
  NRAS MUTATED     0  34
  NRAS WILD-TYPE  12 354
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   34
  NRAS WILD-TYPE   12  354
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             0             12
  YES           34            354
[1] 2 2
[1] FALSE
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           99                      11  245                   1
D2V11, multiclass
                         clus
vv                        NRAS MUTATED NRAS WILD-TYPE
  MINIMAL (T3)                       4             99
  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 286  36   3  21
D2V12, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           27            286
  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 168 189
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13   21
  NRAS WILD-TYPE  168  189
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  MULTIFOCAL           13            168
  UNIFOCAL             21            189
[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   241
D2V16, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                               21            241
[1] 3 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  26 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5   18
  NRAS WILD-TYPE   26  272
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                5             26
  NOT HISPANIC OR LATINO           18            272
[1] 2 2
[1] FALSE

Clustering(3) Variable = HRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    14   0
  HRAS WILD-TYPE 372  13
  HRAS MUTATED HRAS WILD-TYPE 
            14            385 
  HRAS MUTATED HRAS WILD-TYPE 
             0             13 
$`HRAS MUTATED`
TCGA-BJ-A0Z2 TCGA-BJ-A18Y TCGA-BJ-A2P4 TCGA-BJ-A45D TCGA-DJ-A13M TCGA-DJ-A2QB 
       18.21        23.34         7.04        10.88        17.26        35.18 
TCGA-E3-A3DZ TCGA-EL-A3CZ TCGA-EL-A3ZR TCGA-EL-A4JV TCGA-EM-A22K TCGA-EM-A2CK 
       12.07        58.82        60.16        57.47        15.75        17.88 
TCGA-ET-A2N5 TCGA-ET-A39I 
       58.22        13.74 

$`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         8.25        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         7.56        15.12        17.69        20.71 
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         5.10 
TCGA-BJ-A28X TCGA-BJ-A28Z TCGA-BJ-A290 TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 
       17.52         1.22        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        15.48        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         6.35         6.18        21.63         8.98 
TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME 
        4.93        23.47         0.53         0.10         0.20         0.23 
TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 
       10.68         0.39         0.10        20.22        15.42        36.46 
TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DJ-A13L TCGA-DJ-A13O 
        5.98        15.85        18.54        18.84         9.96        14.07 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V 
      169.32         3.39         8.71        56.19        23.38        18.35 
TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG 
       14.60         8.32        11.01       135.91        30.61        13.12 
TCGA-DJ-A1QH TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO 
        7.99        14.96         7.20         1.45        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         7.99         5.33        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        12.56         8.28        34.85         5.52 
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 
        9.44        37.48        36.46        10.09         7.10        35.90 
TCGA-DJ-A2QA TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       12.43        15.88        15.09        31.04        20.45        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        21.37        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
       18.97         7.76        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3E0 
       24.33        54.90        21.53         2.33        31.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       13.61        13.81         3.02        25.45        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        13.78        13.58        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-A3D0 TCGA-EL-A3D1 
       37.94        57.01        80.91         4.18       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        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       131.15       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       130.72       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-A3ZT 
       82.82        78.97        31.50        53.06        61.22        59.44 
TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 TCGA-EL-A4K4 
       34.72        45.96        37.94        31.04        30.51        53.36 
TCGA-EL-A4K6 TCGA-EL-A4KD TCGA-EL-A4KG TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS 
       44.15        43.59        24.30        27.06        23.90        26.86 
TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
       18.18        20.91        12.36        18.05        19.79        19.46 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22L 
       78.61        57.01        54.08        14.73        14.50        10.45 
TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ 
       14.53        10.65        11.74        11.15        14.24        16.44 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 
       12.07        17.49        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        12.53         9.24        13.91         7.82 
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        47.47        48.20        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        22.09        12.26        16.08        29.19         2.66 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
        0.30        17.98        25.32       132.36        24.72         5.03 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.01        73.74        59.70        31.59        44.25        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        81.34        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        22.03 
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        10.26        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         6.74        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 

  HRAS MUTATED HRAS WILD-TYPE 
          7.04           0.10 
  HRAS MUTATED HRAS WILD-TYPE 
         60.16         169.32 
  HRAS MUTATED HRAS WILD-TYPE 
        18.045         21.040 
[1] "7.0 - 60.2 (18.0)"  "0.1 - 169.3 (21.0)"
[1] "hr="     "2.6e+07"
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     222       44        81        2        30         5
D3V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              8            222
  STAGE II             1             44
  STAGE III            2             81
  STAGE IV             0              2
  STAGE IVA            2             30
  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 112 131 126  15
D3V4, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T1            5            112
  T2            6            131
  T3            3            126
  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 181 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      8    4
  HRAS WILD-TYPE  181  166
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            8            181
  1            4            166
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus               0   1
  HRAS MUTATED     8   1
  HRAS WILD-TYPE 213   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      8    1
  HRAS WILD-TYPE  213    6
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            8            213
  1            1              6
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  HRAS MUTATED    10   4
  HRAS WILD-TYPE 288  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED     10    4
  HRAS WILD-TYPE  288   98
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE           10            288
  MALE              4             98
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  HRAS MUTATED                0                                             6
  HRAS WILD-TYPE              6                                           275
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  HRAS MUTATED                                                                        8
  HRAS WILD-TYPE                                                                     75
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  HRAS MUTATED                                                                     0
  HRAS WILD-TYPE                                                                  30
D3V8, 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                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     275
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             75
  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"
D3V9, binary
                cls
clus               0   1
  HRAS MUTATED     0  14
  HRAS WILD-TYPE  12 374
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   14
  HRAS WILD-TYPE   12  374
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             0             12
  YES           14            374
[1] 2 2
[1] FALSE
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          101                      11  261                   1
D3V11, multiclass
                         clus
vv                        HRAS MUTATED HRAS WILD-TYPE
  MINIMAL (T3)                       2            101
  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 304  35   3  20
D3V12, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            9            304
  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     7   7
  HRAS WILD-TYPE 174 203
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      7    7
  HRAS WILD-TYPE  174  203
            clus
vv           HRAS MUTATED HRAS WILD-TYPE
  MULTIFOCAL            7            174
  UNIFOCAL              7            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   254
D3V16, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                2             36
  BLACK OR AFRICAN AMERICAN            2             16
  WHITE                                8            254
[1] 3 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  31 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   12
  HRAS WILD-TYPE   31  278
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO           12            278
[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  12
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               6              393 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               1               12 
$`EIF1AX MUTATED`
TCGA-BJ-A0ZG TCGA-EL-A3CO TCGA-EM-A1YA TCGA-EM-A2CL TCGA-EM-A3FN TCGA-EM-A4FV 
        7.56        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        18.21        16.34         8.25        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        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         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 
        5.10        17.52         1.22        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        15.48 
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         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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        17.26        14.07       169.32         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        18.35        14.60         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        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45        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 
        7.99         5.33        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 
       12.56         8.28        34.85         5.52         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         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        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        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        7.76        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       13.61        13.81         3.02        25.45        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        13.78        13.58        31.66        26.73       155.54 
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        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        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       131.15       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       130.72       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        31.50        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        12.36        18.05 
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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP 
       14.24        16.44        17.88        23.51         6.05         2.99 
TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW 
       12.30        13.64        10.49        13.15        22.16        13.84 
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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR 
       16.80        21.01        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        12.53         9.24        13.91 
TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR 
        7.82        21.34         5.33        26.37        22.45        21.53 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
       13.68        47.47        48.20        29.69        32.35        27.09 
TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 
       29.49        22.09        12.26        16.08        29.19         2.66 
TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M 
       58.22        13.74        71.01        80.02        65.36        84.89 
TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T 
       98.56        61.02        58.72        57.11        55.10        59.15 
TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       28.24         5.85         4.18         2.43         5.56        24.72 
TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP 
       38.30        42.25         2.37         4.50        80.81        69.24 
TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV 
       59.87        43.50         0.30        17.98        25.32       132.36 
TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 
       24.72         5.03         4.01        73.74        59.70        31.59 
TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 
       44.25        24.69        68.22       117.40        66.77        81.34 
TCGA-FE-A23A TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB 
       81.83        85.15        85.68        78.77        71.08         4.11 
TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FY-A2QD TCGA-FY-A3BL 
        1.05        22.03         0.92        48.10         1.25        20.42 
TCGA-FY-A3I4 TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 
       17.82         7.82         0.99        16.14        19.56        13.91 
TCGA-FY-A3R7 TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3W9 TCGA-FY-A3WA 
       16.27        15.68        16.57        18.08         0.76        17.06 
TCGA-FY-A40K TCGA-FY-A4B3 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       15.16         1.35        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 
        2.99        20.05        48.92        47.41        10.26        16.90 
TCGA-J8-A3NZ TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3YE TCGA-J8-A4HW TCGA-KS-A41J 
       17.23        43.17        27.19        27.85         2.60        15.68 
TCGA-KS-A4I5 TCGA-KS-A4I9 TCGA-KS-A4IB TCGA-L6-A4EP TCGA-L6-A4ET TCGA-L6-A4EU 
        6.74        87.39        84.72        33.40        21.83         9.50 
TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       36.10        32.45        30.21 

  EIF1AX MUTATED EIF1AX WILD-TYPE 
            7.56             0.10 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
           97.74           169.32 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
          16.485           21.040 
[1] "7.6 - 97.7 (16.5)"  "0.1 - 169.3 (21.0)"
[1] "hr=" "5.8"
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     226       44        82        2        32         6
D4V3, multiclass
           clus
vv          EIF1AX MUTATED EIF1AX WILD-TYPE
  STAGE I                4              226
  STAGE II               1               44
  STAGE III              1               82
  STAGE IV               0                2
  STAGE IVA              0               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
  EIF1AX MUTATED     2   2   2   0
  EIF1AX WILD-TYPE 115 135 127  15
D4V4, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  T1              2              115
  T2              2              135
  T3              2              127
  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 186 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    1
  EIF1AX WILD-TYPE  186  169
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              3              186
  1              1              169
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     2   0
  EIF1AX WILD-TYPE 219   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      2    0
  EIF1AX WILD-TYPE  219    7
   clus
vv  EIF1AX MUTATED EIF1AX WILD-TYPE
  0              2              219
  1              0                7
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     3   3
  EIF1AX WILD-TYPE 295  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    3
  EIF1AX WILD-TYPE  295   99
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  FEMALE              3              295
  MALE                3               99
[1] 2 2
[1] FALSE
                  vv
clus               OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  EIF1AX MUTATED                0                                             2
  EIF1AX WILD-TYPE              6                                           279
                  vv
clus               THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  EIF1AX MUTATED                                                                        4
  EIF1AX WILD-TYPE                                                                     79
                  vv
clus               THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  EIF1AX MUTATED                                                                     0
  EIF1AX WILD-TYPE                                                                  30
D4V8, 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                                                                        6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               79
  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"
D4V9, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   6
  EIF1AX WILD-TYPE  12 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    6
  EIF1AX WILD-TYPE   12  382
     clus
vv    EIF1AX MUTATED EIF1AX WILD-TYPE
  NO               0               12
  YES              6              382
[1] 2 2
[1] FALSE
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          102                      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              102
  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 309  36   3  21
D4V12, multiclass
    clus
vv   EIF1AX MUTATED EIF1AX WILD-TYPE
  R0              4              309
  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 178 208
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      3    2
  EIF1AX WILD-TYPE  178  208
            clus
vv           EIF1AX MUTATED EIF1AX WILD-TYPE
  MULTIFOCAL              3              178
  UNIFOCAL                2              208
[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   260
D4V16, multiclass
[1] "Remove cluster labels:" "EIF1AX MUTATED"        
clus
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               2              316 
      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-A3VL 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A3VM       TCGA-DJ-A4UL       TCGA-DJ-A4UP       TCGA-DJ-A4UT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DJ-A4UW       TCGA-DJ-A4V0       TCGA-DJ-A4V4       TCGA-DJ-A4V5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-DO-A1JZ       TCGA-DO-A1K0       TCGA-DO-A2HM       TCGA-E3-A3DY 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3DZ       TCGA-E3-A3E0       TCGA-E3-A3E1       TCGA-E3-A3E2 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E3-A3E3       TCGA-E3-A3E5       TCGA-E8-A242       TCGA-E8-A2EA 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A413       TCGA-E8-A415       TCGA-E8-A418       TCGA-E8-A419 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A433       TCGA-E8-A436       TCGA-E8-A437       TCGA-E8-A44K 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-E8-A44M       TCGA-EL-A3CL       TCGA-EL-A3CM       TCGA-EL-A3CN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CP       TCGA-EL-A3CR       TCGA-EL-A3CS       TCGA-EL-A3CT 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW       TCGA-EL-A3CX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0       TCGA-EL-A3D1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6       TCGA-EL-A3GO 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR       TCGA-EL-A3GS 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW       TCGA-EL-A3GX 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H1       TCGA-EL-A3H2 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H3       TCGA-EL-A3H4       TCGA-EL-A3H5       TCGA-EL-A3H7 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3H8       TCGA-EL-A3MW       TCGA-EL-A3MX       TCGA-EL-A3MY 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3MZ       TCGA-EL-A3N2       TCGA-EL-A3N3       TCGA-EL-A3T0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T1       TCGA-EL-A3T2       TCGA-EL-A3T3       TCGA-EL-A3T6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3T7       TCGA-EL-A3T8       TCGA-EL-A3T9       TCGA-EL-A3TA 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3TB       TCGA-EL-A3ZH       TCGA-EL-A3ZK       TCGA-EL-A3ZN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A3ZQ       TCGA-EL-A3ZR       TCGA-EL-A3ZT       TCGA-EL-A4JV 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4JW       TCGA-EL-A4JX       TCGA-EL-A4JZ       TCGA-EL-A4K0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4K2       TCGA-EL-A4K4       TCGA-EL-A4K6       TCGA-EL-A4KD 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EL-A4KG       TCGA-EL-A4KH       TCGA-EL-A4KI       TCGA-EM-A22M 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-EM-A22O       TCGA-EM-A2OV       TCGA-EM-A3AI       TCGA-ET-A25G 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25I       TCGA-ET-A25J       TCGA-ET-A25K       TCGA-ET-A25O 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A25R       TCGA-ET-A2MY       TCGA-ET-A2MZ       TCGA-ET-A2N0 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A2N1       TCGA-ET-A2N4       TCGA-ET-A2N5       TCGA-ET-A39I 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39J       TCGA-ET-A39K       TCGA-ET-A39M       TCGA-ET-A39N 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39O       TCGA-ET-A39P       TCGA-ET-A39R       TCGA-ET-A39S 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A39T       TCGA-ET-A3BN       TCGA-ET-A3BO       TCGA-ET-A3BQ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BS       TCGA-ET-A3BT       TCGA-ET-A3BU       TCGA-ET-A3BV 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3BW       TCGA-ET-A3DO       TCGA-ET-A3DP       TCGA-ET-A3DQ 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DR       TCGA-ET-A3DS       TCGA-ET-A3DT       TCGA-ET-A3DU 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-ET-A3DV       TCGA-ET-A3DW       TCGA-ET-A40S       TCGA-ET-A4KN 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A22Z       TCGA-FE-A230       TCGA-FE-A231       TCGA-FE-A232 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A233       TCGA-FE-A234       TCGA-FE-A235       TCGA-FE-A236 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A237       TCGA-FE-A23A       TCGA-FE-A3PB       TCGA-FE-A3PC 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FE-A3PD       TCGA-FK-A3S3       TCGA-FK-A3SB       TCGA-FK-A3SD 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FK-A3SE       TCGA-FK-A3SG       TCGA-FK-A3SH       TCGA-FY-A2QD 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3BL       TCGA-FY-A3I4       TCGA-FY-A3I5       TCGA-FY-A3NM 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3NP       TCGA-FY-A3ON       TCGA-FY-A3R6       TCGA-FY-A3R7 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3R8       TCGA-FY-A3R9       TCGA-FY-A3RA       TCGA-FY-A3W9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-FY-A3WA       TCGA-FY-A40K       TCGA-FY-A4B3       TCGA-GE-A2C6 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-H2-A26U       TCGA-H2-A2K9       TCGA-H2-A3RH       TCGA-H2-A3RI 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-H2-A421       TCGA-IM-A3EB       TCGA-IM-A3ED       TCGA-IM-A3U2 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-IM-A3U3       TCGA-J8-A3NZ       TCGA-J8-A3O0       TCGA-J8-A3O1 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-J8-A3YE       TCGA-J8-A4HW       TCGA-KS-A41J       TCGA-KS-A4I5 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-KS-A4I9       TCGA-KS-A4IB       TCGA-L6-A4EP       TCGA-L6-A4ET 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
      TCGA-L6-A4EU       TCGA-MK-A4N6       TCGA-MK-A4N7       TCGA-MK-A4N9 
"EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" "EIF1AX WILD-TYPE" 
D4V17, binary
                  cls
clus                 0   1
  EIF1AX MUTATED     0   2
  EIF1AX WILD-TYPE  31 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF1AX MUTATED      0    2
  EIF1AX WILD-TYPE   31  288
                        clus
vv                       EIF1AX MUTATED EIF1AX WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              2              288
[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  13
  NUP93 MUTATED NUP93 WILD-TYPE 
              4             395 
  NUP93 MUTATED NUP93 WILD-TYPE 
              0              13 
$`NUP93 MUTATED`
TCGA-BJ-A191 TCGA-DJ-A2Q4 TCGA-EM-A4FQ TCGA-L6-A4EU 
        4.83         9.44        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        18.21        16.34         8.25        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         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       23.34        20.71        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 
        5.10        17.52         1.22        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        15.48 
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         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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        17.26        14.07       169.32         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        18.35        14.60         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        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45        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 
        7.99         5.33        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 
       12.56         8.28        34.85         5.52         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 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        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        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37        23.21        24.82        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT 
       24.20        17.23        27.62        18.21        21.34        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 
       63.19        30.31        14.04        31.23        22.29        13.61 
TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 
       13.81         3.02        25.45        14.70        14.96         7.69 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       13.78        13.58        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        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        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       131.15       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       130.72       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        31.50        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        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        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        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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        16.80        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 
       12.53         9.24        13.91         7.82        21.34         5.33 
TCGA-EM-A4FO TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       26.37        21.53        24.46        13.68        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       29.69        32.35        27.09        29.49        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       17.98        25.32       132.36        24.72         5.03         4.01 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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        22.03         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        10.26        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         6.74        87.39        84.72 
TCGA-L6-A4EP TCGA-L6-A4ET TCGA-MK-A4N6 TCGA-MK-A4N7 TCGA-MK-A4N9 
       33.40        21.83        36.10        32.45        30.21 

  NUP93 MUTATED NUP93 WILD-TYPE 
           4.83            0.10 
  NUP93 MUTATED NUP93 WILD-TYPE 
          22.45          169.32 
  NUP93 MUTATED NUP93 WILD-TYPE 
           9.47           21.04 
[1] "4.8 - 22.4 (9.5)"   "0.1 - 169.3 (21.0)"
[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     228       45        81        2        32         6
D5V3, multiclass
           clus
vv          NUP93 MUTATED NUP93 WILD-TYPE
  STAGE I               2             228
  STAGE II              0              45
  STAGE III             2              81
  STAGE IV              0               2
  STAGE IVA             0              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
  NUP93 MUTATED     2   1   1   0
  NUP93 WILD-TYPE 115 136 128  15
D5V4, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  T1             2             115
  T2             1             136
  T3             1             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"
D5V5, binary
                 cls
clus                0   1
  NUP93 MUTATED     1   3
  NUP93 WILD-TYPE 188 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      1    3
  NUP93 WILD-TYPE  188  167
   clus
vv  NUP93 MUTATED NUP93 WILD-TYPE
  0             1             188
  1             3             167
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   0
  NUP93 WILD-TYPE 218   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    0
  NUP93 WILD-TYPE  218    7
   clus
vv  NUP93 MUTATED NUP93 WILD-TYPE
  0             3             218
  1             0               7
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  NUP93 MUTATED     3   1
  NUP93 WILD-TYPE 295 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  295  101
        clus
vv       NUP93 MUTATED NUP93 WILD-TYPE
  FEMALE             3             295
  MALE               1             101
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NUP93 MUTATED                1                                             1
  NUP93 WILD-TYPE              5                                           280
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NUP93 MUTATED                                                                        1
  NUP93 WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NUP93 MUTATED                                                                     1
  NUP93 WILD-TYPE                                                                  29
D5V8, 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                                                                       5
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      280
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  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"
D5V9, binary
                 cls
clus                0   1
  NUP93 MUTATED     0   4
  NUP93 WILD-TYPE  12 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      0    4
  NUP93 WILD-TYPE   12  384
     clus
vv    NUP93 MUTATED NUP93 WILD-TYPE
  NO              0              12
  YES             4             384
[1] 2 2
[1] FALSE
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          102                      11  269                   1
D5V11, multiclass
                         clus
vv                        NUP93 MUTATED NUP93 WILD-TYPE
  MINIMAL (T3)                        1             102
  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 310  36   3  22
D5V12, multiclass
    clus
vv   NUP93 MUTATED NUP93 WILD-TYPE
  R0             3             310
  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 178 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      3    1
  NUP93 WILD-TYPE  178  209
            clus
vv           NUP93 MUTATED NUP93 WILD-TYPE
  MULTIFOCAL             3             178
  UNIFOCAL               1             209
[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   260
D5V16, multiclass
                           clus
vv                          NUP93 MUTATED NUP93 WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 2             260
[1] 3 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  31 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP93 MUTATED      0    3
  NUP93 WILD-TYPE   31  287
                        clus
vv                       NUP93 MUTATED NUP93 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             3             287
[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  13
  PPM1D MUTATED PPM1D WILD-TYPE 
              4             395 
  PPM1D MUTATED PPM1D WILD-TYPE 
              0              13 
$`PPM1D MUTATED`
TCGA-DJ-A1QL TCGA-DJ-A2PW TCGA-E8-A418 TCGA-ET-A3BW 
        7.20        34.85         3.02         2.37 

$`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        18.21        16.34         8.25        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         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         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         5.10        17.52         1.22        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 
       15.48        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 
        6.35         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
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        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96         1.45        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 
        7.99         5.33        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 
       12.56         8.28         5.52         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         9.44        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       10.09         7.10        35.90        12.43        35.18        15.88 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       15.09        31.04        20.45        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        24.23        17.69        59.57        11.34 
TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE TCGA-DJ-A3VF 
       21.37        23.21        24.82        22.92        18.97         7.76 
TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP TCGA-DJ-A4UT 
       24.20        17.23        27.62        18.21        21.34        14.14 
TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 TCGA-DO-A1JZ 
       14.70        17.82         3.12        15.81        24.33        54.90 
TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       21.53         2.33        31.07        12.07        66.38        40.21 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A413 
       63.19        30.31        14.04        31.23        22.29        13.61 
TCGA-E8-A415 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K 
       13.81        25.45        14.70        14.96         7.69        13.78 
TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP 
       13.58        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 
       80.91         4.18        58.82       139.86        98.53        45.40 
TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR 
       57.11       108.36        64.87         1.41        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-A3H1 TCGA-EL-A3H2 TCGA-EL-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 
      139.99        49.32        33.50        43.36        49.71        83.57 
TCGA-EL-A3H7 TCGA-EL-A3H8 TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MY TCGA-EL-A3MZ 
      139.00       131.15       108.66        57.63        17.52        52.50 
TCGA-EL-A3N2 TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 TCGA-EL-A3T3 
       29.65       147.42       130.72       129.57        32.48       132.07 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT 
       78.97        31.50        53.06        61.22        60.16        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 
       57.47        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        12.36        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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        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        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        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        16.80        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        12.53 
TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO 
        9.24        13.91         7.82        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        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       29.69        32.35        27.09        29.49        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BX 
        2.43         5.56        24.72        38.30        42.25         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       25.32       132.36        24.72         5.03         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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        22.03         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 
       10.26        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         6.74        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 

  PPM1D MUTATED PPM1D WILD-TYPE 
           2.37            0.10 
  PPM1D MUTATED PPM1D WILD-TYPE 
          34.85          169.32 
  PPM1D MUTATED PPM1D WILD-TYPE 
           5.11           21.04 
[1] "2.4 - 34.9 (5.1)"   "0.1 - 169.3 (21.0)"
[1] "hr="     "1200000"
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     229       44        81        2        31         6
D6V3, multiclass
           clus
vv          PPM1D MUTATED PPM1D WILD-TYPE
  STAGE I               1             229
  STAGE II              1              44
  STAGE III             2              81
  STAGE IV              0               2
  STAGE IVA             1              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
  PPM1D MUTATED     1   2   1   1
  PPM1D WILD-TYPE 116 135 128  14
D6V4, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  T1             1             116
  T2             2             135
  T3             1             128
  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 187 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    2
  PPM1D WILD-TYPE  187  168
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             2             187
  1             2             168
[1] 2 2
[1] FALSE
D6V6, binary
                 cls
clus                0   1
  PPM1D MUTATED     3   0
  PPM1D WILD-TYPE 218   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      3    0
  PPM1D WILD-TYPE  218    7
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             3             218
  1             0               7
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  PPM1D MUTATED     3   2
  PPM1D WILD-TYPE 295 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      3    2
  PPM1D WILD-TYPE  295  100
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  FEMALE             3             295
  MALE               2             100
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  PPM1D MUTATED                0                                             4
  PPM1D WILD-TYPE              6                                           277
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  PPM1D MUTATED                                                                        1
  PPM1D WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  PPM1D MUTATED                                                                     0
  PPM1D WILD-TYPE                                                                  30
D6V8, 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                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      277
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  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"
D6V9, binary
                 cls
clus                0   1
  PPM1D MUTATED     0   5
  PPM1D WILD-TYPE  12 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    5
  PPM1D WILD-TYPE   12  383
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              0              12
  YES             5             383
[1] 2 2
[1] FALSE
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          103                      10  268                   1
D6V11, multiclass
                         clus
vv                        PPM1D MUTATED PPM1D WILD-TYPE
  MINIMAL (T3)                        0             103
  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 309  37   3  21
D6V12, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  R0             4             309
  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             301 
     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-DE-A0XZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DE-A0Y2      TCGA-DE-A0Y3      TCGA-DE-A3KN      TCGA-DE-A4M8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13M      TCGA-DJ-A13O      TCGA-DJ-A13R      TCGA-DJ-A13T 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A13V      TCGA-DJ-A13W      TCGA-DJ-A13X      TCGA-DJ-A1QG 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A1QH      TCGA-DJ-A1QM      TCGA-DJ-A2PO      TCGA-DJ-A2PP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PQ      TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PT 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PU      TCGA-DJ-A2PV      TCGA-DJ-A2PX      TCGA-DJ-A2PY 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q3      TCGA-DJ-A2Q4      TCGA-DJ-A2Q5      TCGA-DJ-A2Q6 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2Q7      TCGA-DJ-A2Q8      TCGA-DJ-A2Q9      TCGA-DJ-A2QA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A2QB      TCGA-DJ-A3UK      TCGA-DJ-A3UM      TCGA-DJ-A3UN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UO      TCGA-DJ-A3UP      TCGA-DJ-A3UQ      TCGA-DJ-A3UR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3UU      TCGA-DJ-A3UW      TCGA-DJ-A3UX      TCGA-DJ-A3V7 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3VA      TCGA-DJ-A3VB      TCGA-DJ-A3VF      TCGA-DJ-A3VJ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A3VL      TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-DJ-A4V2      TCGA-DJ-A4V5      TCGA-DO-A1K0      TCGA-DO-A2HM 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A242 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A2EA      TCGA-E8-A415      TCGA-E8-A419      TCGA-E8-A433 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-E8-A436      TCGA-E8-A44K      TCGA-EL-A3CM      TCGA-EL-A3CN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CO      TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GS      TCGA-EL-A3GU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3GV      TCGA-EL-A3GX      TCGA-EL-A3H3      TCGA-EL-A3H4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3MX      TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3T0 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3TB      TCGA-EL-A3ZH 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A4JV      TCGA-EL-A4JW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EL-A4KI      TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YC      TCGA-EM-A1YD 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22L      TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A22P      TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2CU      TCGA-EM-A2OV      TCGA-EM-A2OX      TCGA-EM-A2OY 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A2OZ      TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3AO      TCGA-EM-A3AQ      TCGA-EM-A3AR      TCGA-EM-A3FJ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FK      TCGA-EM-A3FL      TCGA-EM-A3FM      TCGA-EM-A3FN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3FO      TCGA-EM-A3FP      TCGA-EM-A3FQ      TCGA-EM-A3FR 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3O3      TCGA-EM-A3O8      TCGA-EM-A3O9      TCGA-EM-A3OA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A3OB      TCGA-EM-A4FM      TCGA-EM-A4FO      TCGA-EM-A4FQ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-EM-A4FR      TCGA-EM-A4FV      TCGA-EM-A4G1      TCGA-ET-A25G 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A25I      TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39K      TCGA-ET-A39L      TCGA-ET-A39O      TCGA-ET-A39P 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A39R      TCGA-ET-A39S      TCGA-ET-A39T      TCGA-ET-A3BO 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BP      TCGA-ET-A3BQ      TCGA-ET-A3BS      TCGA-ET-A3BT 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3BU      TCGA-ET-A3BV      TCGA-ET-A3BX      TCGA-ET-A3DQ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3DR      TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DU 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-ET-A3DV      TCGA-ET-A3DW      TCGA-ET-A40S      TCGA-ET-A4KN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A233      TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A237      TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PC 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FE-A3PD      TCGA-FK-A3S3      TCGA-FK-A3SB      TCGA-FK-A3SE 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FK-A3SG      TCGA-FK-A3SH      TCGA-FY-A2QD      TCGA-FY-A3I4 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3I5      TCGA-FY-A3NM      TCGA-FY-A3ON      TCGA-FY-A3R6 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A3R7      TCGA-FY-A3R9      TCGA-FY-A3W9      TCGA-FY-A40K 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-FY-A4B3      TCGA-GE-A2C6      TCGA-H2-A26U      TCGA-H2-A2K9 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-H2-A3RH      TCGA-H2-A3RI      TCGA-H2-A421      TCGA-IM-A3EB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IM-A3ED      TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3NZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-J8-A3O0      TCGA-J8-A3O1      TCGA-J8-A3YE      TCGA-J8-A4HW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-KS-A41J      TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L6-A4EP      TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-MK-A4N9 
"PPM1D WILD-TYPE" 
D6V14, binary
                 cls
clus                0   1
  PPM1D MUTATED     2   3
  PPM1D WILD-TYPE 179 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      2    3
  PPM1D WILD-TYPE  179  207
            clus
vv           PPM1D MUTATED PPM1D WILD-TYPE
  MULTIFOCAL             2             179
  UNIFOCAL               3             207
[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   259
D6V16, multiclass
                           clus
vv                          PPM1D MUTATED PPM1D WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             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"
D6V17, binary
                 cls
clus                0   1
  PPM1D MUTATED     0   4
  PPM1D WILD-TYPE  31 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    4
  PPM1D WILD-TYPE   31  286
                        clus
vv                       PPM1D MUTATED PPM1D WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             4             286
[1] 2 2
[1] FALSE

Clustering(7) Variable = DNMT3A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 384  12
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               3              396 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               1               12 
$`DNMT3A MUTATED`
TCGA-DJ-A2Q2 TCGA-EL-A3CR TCGA-FY-A3NM 
        6.77         7.66         0.99 

$`DNMT3A WILD-TYPE`
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        18.21        16.34         8.25        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         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         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         5.10        17.52         1.22        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 
       15.48        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 
        6.35         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
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        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45        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         7.99         5.33        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        12.56         8.28        34.85         5.52         8.78 
TCGA-DJ-A2PZ TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
        8.42        34.36        37.74        40.24         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        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        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        7.76        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       13.61        13.81         3.02        25.45        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        13.78        13.58        31.66        26.73       155.54 
TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU TCGA-EL-A3CV 
       97.74       158.83        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        80.91         4.18        58.82       139.86        98.53 
TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GQ 
       45.40        57.11       108.36        64.87         1.41        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       131.15       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       130.72       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        31.50        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        12.36        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        11.74 
TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN 
       11.15        14.24        16.44        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        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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        16.80        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 
       12.53         9.24        13.91         7.82        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        47.47 
TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY 
       48.20        29.69        32.35        27.09        29.49        22.09 
TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I 
       12.26        16.08        29.19         2.66        58.22        13.74 
TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O 
       71.01        80.02        65.36        84.89        98.56        61.02 
TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO 
       58.72        57.11        55.10        59.15        28.24         5.85 
TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV 
        4.18         2.43         5.56        24.72        38.30        42.25 
TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR 
        2.37         4.50        80.81        69.24        59.87        43.50 
TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S 
        0.30        17.98        25.32       132.36        24.72         5.03 
TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
        4.01        73.74        59.70        31.59        44.25        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        81.34        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        22.03 
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-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        10.26        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         6.74        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 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            0.99             0.10 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
            7.66           169.32 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
            6.77            21.19 
[1] "1.0 - 7.7 (6.8)"    "0.1 - 169.3 (21.2)"
[1] "hr=" "250"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  DNMT3A MUTATED         0        0         3        0         0         0
  DNMT3A WILD-TYPE     230       45        80        2        32         6
D7V3, multiclass
           clus
vv          DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                0              230
  STAGE II               0               45
  STAGE III              3               80
  STAGE IV               0                2
  STAGE IVA              0               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
  DNMT3A MUTATED     0   0   3   0
  DNMT3A WILD-TYPE 117 137 126  15
D7V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              0              117
  T2              0              137
  T3              3              126
  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
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 187 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2    1
  DNMT3A WILD-TYPE  187  169
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0              2              187
  1              1              169
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     2   0
  DNMT3A WILD-TYPE 219   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2    0
  DNMT3A WILD-TYPE  219    7
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0              2              219
  1              0                7
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     3   0
  DNMT3A WILD-TYPE 295 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      3    0
  DNMT3A WILD-TYPE  295  102
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              3              295
  MALE                0              102
[1] 2 2
[1] FALSE
                  vv
clus               OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DNMT3A MUTATED                0                                             2
  DNMT3A WILD-TYPE              6                                           279
                  vv
clus               THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DNMT3A MUTATED                                                                        1
  DNMT3A WILD-TYPE                                                                     82
                  vv
clus               THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DNMT3A MUTATED                                                                     0
  DNMT3A WILD-TYPE                                                                  30
D7V8, multiclass
                                                                        clus
vv                                                                       DNMT3A 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                                                                       DNMT3A WILD-TYPE
  OTHER  SPECIFY                                                                        6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                       279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)               82
  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"
D7V9, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0   3
  DNMT3A WILD-TYPE  12 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0    3
  DNMT3A WILD-TYPE   12  385
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               0               12
  YES              3              385
[1] 2 2
[1] FALSE
D7V10, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     2   1
  DNMT3A WILD-TYPE 334  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2    1
  DNMT3A WILD-TYPE  334   14
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO               2              334
  YES              1               14
[1] 2 2
[1] FALSE
                  vv
clus               MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE
  DNMT3A MUTATED              2                       0    1
  DNMT3A WILD-TYPE          101                      11  271
                  vv
clus               VERY ADVANCED (T4B)
  DNMT3A MUTATED                     0
  DNMT3A WILD-TYPE                   1
D7V11, multiclass
                         clus
vv                        DNMT3A MUTATED DNMT3A WILD-TYPE
  MINIMAL (T3)                         2              101
  MODERATE/ADVANCED (T4A)              0               11
  NONE                                 1              271
  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
  DNMT3A MUTATED     2   1   0   0
  DNMT3A WILD-TYPE 311  36   3  22
D7V12, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  R0              2              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"
D7V13, continuous
D7V14, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     1   2
  DNMT3A WILD-TYPE 180 208
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    2
  DNMT3A WILD-TYPE  180  208
            clus
vv           DNMT3A MUTATED DNMT3A WILD-TYPE
  MULTIFOCAL              1              180
  UNIFOCAL                2              208
[1] 2 2
[1] FALSE
D7V15, continuous
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2              324 
      TCGA-BJ-A0Z2       TCGA-BJ-A0Z3       TCGA-BJ-A0Z9       TCGA-BJ-A0ZA 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZB       TCGA-BJ-A0ZC       TCGA-BJ-A0ZE       TCGA-BJ-A0ZG 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A0ZH       TCGA-BJ-A0ZJ       TCGA-BJ-A18Y       TCGA-BJ-A18Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A191       TCGA-BJ-A192       TCGA-BJ-A28R       TCGA-BJ-A28S 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A28T       TCGA-BJ-A28V       TCGA-BJ-A28Z       TCGA-BJ-A290 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A2N8       TCGA-BJ-A2N9       TCGA-BJ-A2P4       TCGA-BJ-A3PU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A45D       TCGA-BJ-A45E       TCGA-BJ-A45F       TCGA-BJ-A45G 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A45I       TCGA-BJ-A45J       TCGA-BJ-A45K       TCGA-BJ-A4O8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-BJ-A4O9       TCGA-CE-A13K       TCGA-CE-A27D       TCGA-CE-A3MD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CE-A3ME       TCGA-CE-A482       TCGA-CE-A484       TCGA-CE-A485 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A0XZ       TCGA-DE-A0Y2       TCGA-DE-A0Y3       TCGA-DE-A2OL 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DE-A3KN       TCGA-DE-A4M8       TCGA-DE-A4M9       TCGA-DJ-A13L 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13M       TCGA-DJ-A13O       TCGA-DJ-A13R       TCGA-DJ-A13S 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A13U       TCGA-DJ-A13V       TCGA-DJ-A13W       TCGA-DJ-A13X 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QD       TCGA-DJ-A1QE       TCGA-DJ-A1QF       TCGA-DJ-A1QG 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QH       TCGA-DJ-A1QI       TCGA-DJ-A1QL       TCGA-DJ-A1QM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A1QN       TCGA-DJ-A1QO       TCGA-DJ-A1QQ       TCGA-DJ-A2PN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PO       TCGA-DJ-A2PP       TCGA-DJ-A2PQ       TCGA-DJ-A2PR 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PS       TCGA-DJ-A2PT       TCGA-DJ-A2PU       TCGA-DJ-A2PV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2PW       TCGA-DJ-A2PY       TCGA-DJ-A2PZ       TCGA-DJ-A2Q0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q1       TCGA-DJ-A2Q3       TCGA-DJ-A2Q4       TCGA-DJ-A2Q5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2Q6       TCGA-DJ-A2Q7       TCGA-DJ-A2Q8       TCGA-DJ-A2Q9 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A2QA       TCGA-DJ-A2QC       TCGA-DJ-A3UK       TCGA-DJ-A3UM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3UN       TCGA-DJ-A3UO       TCGA-DJ-A3UP       TCGA-DJ-A3UQ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3UR       TCGA-DJ-A3US       TCGA-DJ-A3UT       TCGA-DJ-A3UU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3UW       TCGA-DJ-A3UX       TCGA-DJ-A3UY       TCGA-DJ-A3V7 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3VA       TCGA-DJ-A3VB       TCGA-DJ-A3VE       TCGA-DJ-A3VF 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A3VJ       TCGA-DJ-A3VL       TCGA-DJ-A3VM       TCGA-DJ-A4UL 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A4UP       TCGA-DJ-A4UT       TCGA-DJ-A4V0       TCGA-DJ-A4V2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DJ-A4V4       TCGA-DJ-A4V5       TCGA-DO-A1JZ       TCGA-DO-A1K0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DO-A2HM       TCGA-E3-A3DY       TCGA-E3-A3DZ       TCGA-E3-A3E0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-E3-A3E1       TCGA-E3-A3E2       TCGA-E3-A3E3       TCGA-E8-A419 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CN       TCGA-EL-A3CO       TCGA-EL-A3CS       TCGA-EL-A3CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CU       TCGA-EL-A3CV       TCGA-EL-A3CW       TCGA-EL-A3CX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3CY       TCGA-EL-A3CZ       TCGA-EL-A3D0       TCGA-EL-A3D1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3D4       TCGA-EL-A3D5       TCGA-EL-A3D6       TCGA-EL-A3GO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GP       TCGA-EL-A3GQ       TCGA-EL-A3GR       TCGA-EL-A3GS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GU       TCGA-EL-A3GV       TCGA-EL-A3GW       TCGA-EL-A3GX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3GY       TCGA-EL-A3GZ       TCGA-EL-A3H2       TCGA-EL-A3H3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3H4       TCGA-EL-A3H5       TCGA-EL-A3H7       TCGA-EL-A3H8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3MW       TCGA-EL-A3MX       TCGA-EL-A3MY       TCGA-EL-A3MZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3N2       TCGA-EL-A3N3       TCGA-EL-A3T1       TCGA-EL-A3T2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3T3       TCGA-EL-A3T6       TCGA-EL-A3T7       TCGA-EL-A3T8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3T9       TCGA-EL-A3TA       TCGA-EL-A3TB       TCGA-EL-A3ZH 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3ZK       TCGA-EL-A3ZN       TCGA-EL-A3ZQ       TCGA-EL-A3ZR 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A3ZT       TCGA-EL-A4JV       TCGA-EL-A4JW       TCGA-EL-A4JX 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4JZ       TCGA-EL-A4K0       TCGA-EL-A4K2       TCGA-EL-A4K4 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4K6       TCGA-EL-A4KD       TCGA-EL-A4KG       TCGA-EL-A4KH 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EL-A4KI       TCGA-EM-A1CS       TCGA-EM-A1CT       TCGA-EM-A1CU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1CV       TCGA-EM-A1CW       TCGA-EM-A1YA       TCGA-EM-A1YB 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A1YC       TCGA-EM-A1YD       TCGA-EM-A1YE       TCGA-EM-A22I 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22J       TCGA-EM-A22K       TCGA-EM-A22L       TCGA-EM-A22N 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A22O       TCGA-EM-A22P       TCGA-EM-A22Q       TCGA-EM-A2CJ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CK       TCGA-EM-A2CL       TCGA-EM-A2CN       TCGA-EM-A2CO 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CP       TCGA-EM-A2CQ       TCGA-EM-A2CR       TCGA-EM-A2CT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2CU       TCGA-EM-A2OW       TCGA-EM-A2OX       TCGA-EM-A2OY 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A2P0       TCGA-EM-A2P1       TCGA-EM-A2P2       TCGA-EM-A2P3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AI       TCGA-EM-A3AJ       TCGA-EM-A3AK       TCGA-EM-A3AL 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AN       TCGA-EM-A3AO       TCGA-EM-A3AP       TCGA-EM-A3AQ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3AR       TCGA-EM-A3FJ       TCGA-EM-A3FM       TCGA-EM-A3FN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3FO       TCGA-EM-A3FP       TCGA-EM-A3FR       TCGA-EM-A3O3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3O6       TCGA-EM-A3O7       TCGA-EM-A3O8       TCGA-EM-A3O9 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A3OA       TCGA-EM-A3OB       TCGA-EM-A4FK       TCGA-EM-A4FM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EM-A4FQ       TCGA-EM-A4FR       TCGA-EM-A4FV       TCGA-EM-A4G1 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A25G       TCGA-ET-A25I       TCGA-ET-A25J       TCGA-ET-A25K 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A25O       TCGA-ET-A25R       TCGA-ET-A2MY       TCGA-ET-A2MZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A2N0       TCGA-ET-A2N5       TCGA-ET-A39J       TCGA-ET-A39M 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A39N       TCGA-ET-A39O       TCGA-ET-A39P       TCGA-ET-A39T 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BN       TCGA-ET-A3BO       TCGA-ET-A3BP       TCGA-ET-A3BQ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BS       TCGA-ET-A3BT       TCGA-ET-A3BU       TCGA-ET-A3BV 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3BW       TCGA-ET-A3BX       TCGA-ET-A3DO       TCGA-ET-A3DS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-ET-A3DT       TCGA-ET-A40S       TCGA-ET-A4KN       TCGA-FE-A22Z 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A230       TCGA-FE-A232       TCGA-FE-A233       TCGA-FE-A234 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A235       TCGA-FE-A236       TCGA-FE-A237       TCGA-FE-A23A 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FE-A3PB       TCGA-FE-A3PC       TCGA-FE-A3PD       TCGA-FY-A2QD 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FY-A3I4       TCGA-FY-A3I5       TCGA-FY-A3ON       TCGA-FY-A3R8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-FY-A3W9       TCGA-FY-A40K       TCGA-FY-A4B3       TCGA-GE-A2C6 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-H2-A421       TCGA-IM-A3EB       TCGA-IM-A3ED       TCGA-IM-A3U2 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-IM-A3U3       TCGA-J8-A3O0       TCGA-KS-A41J       TCGA-KS-A4I5 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KS-A4I9       TCGA-KS-A4IB       TCGA-L6-A4EP       TCGA-L6-A4ET 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-L6-A4EU       TCGA-MK-A4N6       TCGA-MK-A4N7       TCGA-MK-A4N9 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED       0                         0     3
  DNMT3A WILD-TYPE    38                        18   259
D7V16, multiclass
                           clus
vv                          DNMT3A MUTATED DNMT3A WILD-TYPE
  ASIAN                                  0               38
  BLACK OR AFRICAN AMERICAN              0               18
  WHITE                                  3              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"
D7V17, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0   3
  DNMT3A WILD-TYPE  31 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0    3
  DNMT3A WILD-TYPE   31  287
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              3              287
[1] 2 2
[1] FALSE

Clustering(8) Variable = KRAS MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 382  13
  KRAS MUTATED KRAS WILD-TYPE 
             4            395 
  KRAS MUTATED KRAS WILD-TYPE 
             0             13 
$`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        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
        4.01        11.57         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         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 
        5.10        17.52         1.22        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        15.48 
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         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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        17.26        14.07       169.32         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        18.35        14.60         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        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45        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 
        7.99         5.33        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 
       12.56         8.28        34.85         5.52         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         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        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        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        7.76        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       13.61        13.81         3.02        25.45        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        13.78        13.58        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        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
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       131.15       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       130.72       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        31.50        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        12.36 
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 
       11.74        11.15        14.24        16.44        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CR TCGA-EM-A2CT TCGA-EM-A2CU 
       23.51         6.05         2.99        13.64        10.49        13.15 
TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 
       22.16        13.84        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        16.80        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 
       12.53         9.24        13.91         7.82        21.34         5.33 
TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I 
       26.37        22.45        21.53        13.68        47.47        48.20 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ 
       29.69        32.35        27.09        29.49        22.09        12.26 
TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J 
       16.08        29.19         2.66        58.22        13.74        71.01 
TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
       80.02        65.36        84.89        98.56        61.02        58.72 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
       57.11        55.10        59.15        28.24         5.85         4.18 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW 
        2.43         5.56        24.72        38.30        42.25         2.37 
TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS 
        4.50        80.81        69.24        59.87        43.50         0.30 
TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN 
       17.98        25.32       132.36        24.72         5.03         4.01 
TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 
       73.74        59.70        31.59        44.25        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        81.34        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        22.03         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-A3RI TCGA-H2-A421 TCGA-IM-A3EB TCGA-IM-A3ED 
       17.00        21.67         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 
       10.26        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         6.74        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 

  KRAS MUTATED KRAS WILD-TYPE 
          12.3            0.1 
  KRAS MUTATED KRAS WILD-TYPE 
         24.46         169.32 
  KRAS MUTATED KRAS WILD-TYPE 
        14.595         21.040 
[1] "12.3 - 24.5 (14.6)" "0.1 - 169.3 (21.0)"
[1] "hr="     "1200000"
D8V2, 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     227       45        82        2        32         6
D8V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              3            227
  STAGE II             0             45
  STAGE III            1             82
  STAGE IV             0              2
  STAGE IVA            0             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
  KRAS MUTATED     3   0   1   0
  KRAS WILD-TYPE 114 137 128  15
D8V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            3            114
  T2            0            137
  T3            1            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"
D8V5, binary
                cls
clus               0   1
  KRAS MUTATED     3   1
  KRAS WILD-TYPE 186 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      3    1
  KRAS WILD-TYPE  186  169
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            3            186
  1            1            169
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus               0   1
  KRAS MUTATED     2   0
  KRAS WILD-TYPE 219   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    0
  KRAS WILD-TYPE  219    7
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            2            219
  1            0              7
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  KRAS MUTATED     4   0
  KRAS WILD-TYPE 294 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    0
  KRAS WILD-TYPE  294  102
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            4            294
  MALE              0            102
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  KRAS MUTATED                0                                             2
  KRAS WILD-TYPE              6                                           279
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  KRAS MUTATED                                                                        2
  KRAS WILD-TYPE                                                                     81
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  KRAS MUTATED                                                                     0
  KRAS WILD-TYPE                                                                  30
D8V8, 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                                                                      6
  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"
D8V9, binary
                cls
clus               0   1
  KRAS MUTATED     0   4
  KRAS WILD-TYPE  12 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    4
  KRAS WILD-TYPE   12  384
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             0             12
  YES            4            384
[1] 2 2
[1] FALSE
D8V10, 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          102                      11  269                   1
D8V11, multiclass
                         clus
vv                        KRAS MUTATED KRAS WILD-TYPE
  MINIMAL (T3)                       1            102
  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 311  36   3  22
D8V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0            2            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
D8V14, binary
                cls
clus               0   1
  KRAS MUTATED     2   2
  KRAS WILD-TYPE 179 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    2
  KRAS WILD-TYPE  179  208
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  MULTIFOCAL            2            179
  UNIFOCAL              2            208
[1] 2 2
[1] FALSE
D8V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     2
  KRAS WILD-TYPE    38                        18   260
D8V16, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            316 
    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-A3VL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A3VM     TCGA-DJ-A4UL     TCGA-DJ-A4UP     TCGA-DJ-A4UT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DJ-A4UW     TCGA-DJ-A4V0     TCGA-DJ-A4V4     TCGA-DJ-A4V5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DO-A1JZ     TCGA-DO-A1K0     TCGA-DO-A2HM     TCGA-E3-A3DY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3DZ     TCGA-E3-A3E0     TCGA-E3-A3E1     TCGA-E3-A3E2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E3-A3E3     TCGA-E3-A3E5     TCGA-E8-A242     TCGA-E8-A2EA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A413     TCGA-E8-A415     TCGA-E8-A418     TCGA-E8-A419 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A433     TCGA-E8-A436     TCGA-E8-A437     TCGA-E8-A44K 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-E8-A44M     TCGA-EL-A3CL     TCGA-EL-A3CM     TCGA-EL-A3CN 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CO     TCGA-EL-A3CP     TCGA-EL-A3CR     TCGA-EL-A3CS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CT     TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3CX     TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3D1     TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GO     TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GS     TCGA-EL-A3GU     TCGA-EL-A3GV     TCGA-EL-A3GW 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3GX     TCGA-EL-A3GY     TCGA-EL-A3GZ     TCGA-EL-A3H1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H2     TCGA-EL-A3H3     TCGA-EL-A3H4     TCGA-EL-A3H5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW     TCGA-EL-A3MX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3MY     TCGA-EL-A3MZ     TCGA-EL-A3N2     TCGA-EL-A3N3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T0     TCGA-EL-A3T1     TCGA-EL-A3T2     TCGA-EL-A3T3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3T6     TCGA-EL-A3T7     TCGA-EL-A3T8     TCGA-EL-A3T9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3TA     TCGA-EL-A3TB     TCGA-EL-A3ZH     TCGA-EL-A3ZK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A3ZN     TCGA-EL-A3ZQ     TCGA-EL-A3ZR     TCGA-EL-A3ZT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4JV     TCGA-EL-A4JW     TCGA-EL-A4JX     TCGA-EL-A4JZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4K0     TCGA-EL-A4K2     TCGA-EL-A4K4     TCGA-EL-A4K6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EL-A4KD     TCGA-EL-A4KG     TCGA-EL-A4KH     TCGA-EL-A4KI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EM-A22M     TCGA-EM-A22O     TCGA-EM-A2OV     TCGA-EM-A3AI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A25G     TCGA-ET-A25I     TCGA-ET-A25J     TCGA-ET-A25K 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A25O     TCGA-ET-A25R     TCGA-ET-A2MY     TCGA-ET-A2MZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4     TCGA-ET-A2N5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39I     TCGA-ET-A39J     TCGA-ET-A39K     TCGA-ET-A39M 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39N     TCGA-ET-A39O     TCGA-ET-A39P     TCGA-ET-A39R 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A39S     TCGA-ET-A39T     TCGA-ET-A3BN     TCGA-ET-A3BO 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BQ     TCGA-ET-A3BS     TCGA-ET-A3BT     TCGA-ET-A3BU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3BV     TCGA-ET-A3BW     TCGA-ET-A3DO     TCGA-ET-A3DP 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DQ     TCGA-ET-A3DR     TCGA-ET-A3DS     TCGA-ET-A3DT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A3DU     TCGA-ET-A3DV     TCGA-ET-A3DW     TCGA-ET-A40S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-ET-A4KN     TCGA-FE-A22Z     TCGA-FE-A230     TCGA-FE-A231 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A232     TCGA-FE-A233     TCGA-FE-A234     TCGA-FE-A235 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A236     TCGA-FE-A237     TCGA-FE-A23A     TCGA-FE-A3PB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FE-A3PC     TCGA-FE-A3PD     TCGA-FK-A3S3     TCGA-FK-A3SB 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FK-A3SD     TCGA-FK-A3SE     TCGA-FK-A3SG     TCGA-FK-A3SH 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A2QD     TCGA-FY-A3BL     TCGA-FY-A3I4     TCGA-FY-A3I5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3NM     TCGA-FY-A3NP     TCGA-FY-A3ON     TCGA-FY-A3R6 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3R7     TCGA-FY-A3R8     TCGA-FY-A3R9     TCGA-FY-A3RA 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-FY-A3W9     TCGA-FY-A3WA     TCGA-FY-A40K     TCGA-FY-A4B3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GE-A2C6     TCGA-H2-A26U     TCGA-H2-A2K9     TCGA-H2-A3RI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-H2-A421     TCGA-IM-A3EB     TCGA-IM-A3ED     TCGA-IM-A3U2 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IM-A3U3     TCGA-J8-A3NZ     TCGA-J8-A3O0     TCGA-J8-A3O1 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J8-A3YE     TCGA-J8-A4HW     TCGA-KS-A41J     TCGA-KS-A4I5 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KS-A4I9     TCGA-KS-A4IB     TCGA-L6-A4EP     TCGA-L6-A4ET 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-L6-A4EU     TCGA-MK-A4N6     TCGA-MK-A4N7     TCGA-MK-A4N9 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D8V17, binary
                cls
clus               0   1
  KRAS MUTATED     0   2
  KRAS WILD-TYPE  31 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    2
  KRAS WILD-TYPE   31  288
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            2            288
[1] 2 2
[1] FALSE

Clustering(9) Variable = DLC1 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 383  12
  DLC1 MUTATED DLC1 WILD-TYPE 
             4            395 
  DLC1 MUTATED DLC1 WILD-TYPE 
             1             12 
$`DLC1 MUTATED`
TCGA-EL-A3CR TCGA-EL-A3N2 TCGA-EL-A3T3 TCGA-EM-A2OW 
        7.66        29.65       132.07        13.84 

$`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        18.21        16.34         8.25        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         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         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         5.10        17.52         1.22        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 
       15.48        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 
        6.35         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
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        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45        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         7.99         5.33        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        12.56         8.28        34.85         5.52         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         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        10.09         7.10        35.90        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        15.09        31.04        20.45        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        21.37        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
       18.97         7.76        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       22.29        13.61        13.81         3.02        25.45        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69        13.78        13.58        31.66        26.73 
TCGA-EL-A3CN TCGA-EL-A3CO TCGA-EL-A3CP TCGA-EL-A3CS TCGA-EL-A3CT TCGA-EL-A3CU 
      155.54        97.74       158.83        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        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
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       131.15       108.66        57.63 
TCGA-EL-A3MY TCGA-EL-A3MZ TCGA-EL-A3N3 TCGA-EL-A3T0 TCGA-EL-A3T1 TCGA-EL-A3T2 
       17.52        52.50       147.42       130.72       129.57        32.48 
TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 TCGA-EL-A3TA TCGA-EL-A3TB 
       98.24        41.29       107.47         5.72        66.90        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT 
       78.97        31.50        53.06        61.22        60.16        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 
       57.47        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        12.36        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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        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        10.49        13.15        22.16 
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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       13.38         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        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        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ 
       13.91         7.82        21.34         5.33        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       21.53        24.46        13.68        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       32.35        27.09        29.49        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       25.32       132.36        24.72         5.03         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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        22.03         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 
       10.26        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         6.74        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 

  DLC1 MUTATED DLC1 WILD-TYPE 
          7.66           0.10 
  DLC1 MUTATED DLC1 WILD-TYPE 
        132.07         169.32 
  DLC1 MUTATED DLC1 WILD-TYPE 
        21.745         21.010 
[1] "7.7 - 132.1 (21.7)" "0.1 - 169.3 (21.0)"
[1] "hr=" "6"  
D9V2, 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     228       44        82        2        32         6
D9V3, multiclass
           clus
vv          DLC1 MUTATED DLC1 WILD-TYPE
  STAGE I              2            228
  STAGE II             1             44
  STAGE III            1             82
  STAGE IV             0              2
  STAGE IVA            0             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
  DLC1 MUTATED     1   2   1   0
  DLC1 WILD-TYPE 116 135 128  15
D9V4, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  T1            1            116
  T2            2            135
  T3            1            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"
D9V5, binary
                cls
clus               0   1
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE 188 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE  188  168
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            1            188
  1            2            168
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus               0   1
  DLC1 MUTATED     3   0
  DLC1 WILD-TYPE 218   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    0
  DLC1 WILD-TYPE  218    7
   clus
vv  DLC1 MUTATED DLC1 WILD-TYPE
  0            3            218
  1            0              7
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  DLC1 MUTATED     3   1
  DLC1 WILD-TYPE 295 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      3    1
  DLC1 WILD-TYPE  295  101
        clus
vv       DLC1 MUTATED DLC1 WILD-TYPE
  FEMALE            3            295
  MALE              1            101
[1] 2 2
[1] FALSE
                vv
clus             OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  DLC1 MUTATED                0                                             3
  DLC1 WILD-TYPE              6                                           278
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  DLC1 MUTATED                                                                        1
  DLC1 WILD-TYPE                                                                     82
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  DLC1 MUTATED                                                                     0
  DLC1 WILD-TYPE                                                                  30
D9V8, 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                                                                      6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                     278
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)             82
  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"
D9V9, binary
                cls
clus               0   1
  DLC1 MUTATED     0   4
  DLC1 WILD-TYPE  12 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      0    4
  DLC1 WILD-TYPE   12  384
     clus
vv    DLC1 MUTATED DLC1 WILD-TYPE
  NO             0             12
  YES            4            384
[1] 2 2
[1] FALSE
D9V10, 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          101                      11  270                   1
D9V11, multiclass
                         clus
vv                        DLC1 MUTATED DLC1 WILD-TYPE
  MINIMAL (T3)                       2            101
  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 310  36   3  22
D9V12, multiclass
    clus
vv   DLC1 MUTATED DLC1 WILD-TYPE
  R0            3            310
  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"
D9V13, continuous
[1] "Remove cluster labels:" "DLC1 MUTATED"          
clus
  DLC1 MUTATED DLC1 WILD-TYPE 
             2            301 
    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-DE-A0XZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DE-A0Y2     TCGA-DE-A0Y3     TCGA-DE-A3KN     TCGA-DE-A4M8 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13M     TCGA-DJ-A13O     TCGA-DJ-A13R     TCGA-DJ-A13T 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A13V     TCGA-DJ-A13W     TCGA-DJ-A13X     TCGA-DJ-A1QG 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A1QH     TCGA-DJ-A1QM     TCGA-DJ-A2PO     TCGA-DJ-A2PP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PQ     TCGA-DJ-A2PR     TCGA-DJ-A2PS     TCGA-DJ-A2PT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PU     TCGA-DJ-A2PV     TCGA-DJ-A2PW     TCGA-DJ-A2PX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2PY     TCGA-DJ-A2PZ     TCGA-DJ-A2Q0     TCGA-DJ-A2Q1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q2     TCGA-DJ-A2Q3     TCGA-DJ-A2Q4     TCGA-DJ-A2Q5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2Q6     TCGA-DJ-A2Q7     TCGA-DJ-A2Q8     TCGA-DJ-A2Q9 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A2QA     TCGA-DJ-A2QB     TCGA-DJ-A3UK     TCGA-DJ-A3UM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3UN     TCGA-DJ-A3UO     TCGA-DJ-A3UP     TCGA-DJ-A3UQ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3UR     TCGA-DJ-A3UU     TCGA-DJ-A3UW     TCGA-DJ-A3UX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3V7     TCGA-DJ-A3VA     TCGA-DJ-A3VB     TCGA-DJ-A3VF 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A3VJ     TCGA-DJ-A3VL     TCGA-DJ-A4UL     TCGA-DJ-A4UP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DJ-A4UW     TCGA-DJ-A4V2     TCGA-DJ-A4V5     TCGA-DO-A1K0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-DO-A2HM     TCGA-E3-A3DY     TCGA-E3-A3DZ     TCGA-E3-A3E0 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E3-A3E1     TCGA-E3-A3E2     TCGA-E3-A3E3     TCGA-E3-A3E5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E8-A242     TCGA-E8-A2EA     TCGA-E8-A415     TCGA-E8-A419 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-E8-A433     TCGA-E8-A436     TCGA-E8-A44K     TCGA-EL-A3CM 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CN     TCGA-EL-A3CO     TCGA-EL-A3CS     TCGA-EL-A3CT 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CU     TCGA-EL-A3CV     TCGA-EL-A3CW     TCGA-EL-A3CX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3CY     TCGA-EL-A3CZ     TCGA-EL-A3D0     TCGA-EL-A3D1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3D4     TCGA-EL-A3D5     TCGA-EL-A3D6     TCGA-EL-A3GO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GP     TCGA-EL-A3GQ     TCGA-EL-A3GS     TCGA-EL-A3GU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3GV     TCGA-EL-A3GX     TCGA-EL-A3H3     TCGA-EL-A3H4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3H5     TCGA-EL-A3H7     TCGA-EL-A3H8     TCGA-EL-A3MW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3MX     TCGA-EL-A3MZ     TCGA-EL-A3T0     TCGA-EL-A3T1 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3T2     TCGA-EL-A3TB     TCGA-EL-A3ZH     TCGA-EL-A3ZK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A3ZN     TCGA-EL-A4JV     TCGA-EL-A4JW     TCGA-EL-A4JX 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A4JZ     TCGA-EL-A4K0     TCGA-EL-A4K2     TCGA-EL-A4K4 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EL-A4K6     TCGA-EL-A4KD     TCGA-EL-A4KG     TCGA-EL-A4KI 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1CS     TCGA-EM-A1CT     TCGA-EM-A1CU     TCGA-EM-A1CV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A1CW     TCGA-EM-A1YC     TCGA-EM-A1YD     TCGA-EM-A1YE 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22I     TCGA-EM-A22J     TCGA-EM-A22K     TCGA-EM-A22L 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22M     TCGA-EM-A22N     TCGA-EM-A22O     TCGA-EM-A22P 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A22Q     TCGA-EM-A2CK     TCGA-EM-A2CN     TCGA-EM-A2CP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2CQ     TCGA-EM-A2CR     TCGA-EM-A2CT     TCGA-EM-A2CU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2OV     TCGA-EM-A2OX     TCGA-EM-A2OY     TCGA-EM-A2OZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A2P0     TCGA-EM-A2P1     TCGA-EM-A2P2     TCGA-EM-A3AJ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AK     TCGA-EM-A3AL     TCGA-EM-A3AN     TCGA-EM-A3AO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3AQ     TCGA-EM-A3AR     TCGA-EM-A3FJ     TCGA-EM-A3FK 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FL     TCGA-EM-A3FM     TCGA-EM-A3FN     TCGA-EM-A3FO 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3FP     TCGA-EM-A3FQ     TCGA-EM-A3FR     TCGA-EM-A3O3 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A3O8     TCGA-EM-A3O9     TCGA-EM-A3OA     TCGA-EM-A3OB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A4FM     TCGA-EM-A4FO     TCGA-EM-A4FQ     TCGA-EM-A4FR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-EM-A4FV     TCGA-EM-A4G1     TCGA-ET-A25G     TCGA-ET-A25I 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A25J     TCGA-ET-A25K     TCGA-ET-A25O     TCGA-ET-A2MZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A2N0     TCGA-ET-A2N1     TCGA-ET-A2N4     TCGA-ET-A39K 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39L     TCGA-ET-A39O     TCGA-ET-A39P     TCGA-ET-A39R 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A39S     TCGA-ET-A39T     TCGA-ET-A3BO     TCGA-ET-A3BP 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BQ     TCGA-ET-A3BS     TCGA-ET-A3BT     TCGA-ET-A3BU 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3BV     TCGA-ET-A3BX     TCGA-ET-A3DQ     TCGA-ET-A3DR 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DS     TCGA-ET-A3DT     TCGA-ET-A3DU     TCGA-ET-A3DV 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-ET-A3DW     TCGA-ET-A40S     TCGA-ET-A4KN     TCGA-FE-A22Z 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A230     TCGA-FE-A231     TCGA-FE-A232     TCGA-FE-A233 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A234     TCGA-FE-A235     TCGA-FE-A236     TCGA-FE-A237 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FE-A23A     TCGA-FE-A3PB     TCGA-FE-A3PC     TCGA-FE-A3PD 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FK-A3S3     TCGA-FK-A3SB     TCGA-FK-A3SE     TCGA-FK-A3SG 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FK-A3SH     TCGA-FY-A2QD     TCGA-FY-A3I4     TCGA-FY-A3I5 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A3NM     TCGA-FY-A3NN     TCGA-FY-A3ON     TCGA-FY-A3R6 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A3R7     TCGA-FY-A3R9     TCGA-FY-A3W9     TCGA-FY-A40K 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-FY-A4B3     TCGA-GE-A2C6     TCGA-H2-A26U     TCGA-H2-A2K9 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-H2-A3RH     TCGA-H2-A3RI     TCGA-H2-A421     TCGA-IM-A3EB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-IM-A3ED     TCGA-IM-A3U2     TCGA-IM-A3U3     TCGA-J8-A3NZ 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-J8-A3O0     TCGA-J8-A3O1     TCGA-J8-A3YE     TCGA-J8-A4HW 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-KS-A41J     TCGA-KS-A4I5     TCGA-KS-A4I9     TCGA-KS-A4IB 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-L6-A4EP     TCGA-L6-A4EU     TCGA-MK-A4N6     TCGA-MK-A4N7 
"DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" "DLC1 WILD-TYPE" 
    TCGA-MK-A4N9 
"DLC1 WILD-TYPE" 
D9V14, binary
                cls
clus               0   1
  DLC1 MUTATED     1   3
  DLC1 WILD-TYPE 180 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    3
  DLC1 WILD-TYPE  180  207
            clus
vv           DLC1 MUTATED DLC1 WILD-TYPE
  MULTIFOCAL            1            180
  UNIFOCAL              3            207
[1] 2 2
[1] FALSE
D9V15, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DLC1 MUTATED       0                         0     3
  DLC1 WILD-TYPE    38                        18   259
D9V16, multiclass
                           clus
vv                          DLC1 MUTATED DLC1 WILD-TYPE
  ASIAN                                0             38
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                3            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"
D9V17, binary
                cls
clus               0   1
  DLC1 MUTATED     1   2
  DLC1 WILD-TYPE  30 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLC1 MUTATED      1    2
  DLC1 WILD-TYPE   30  288
                        clus
vv                       DLC1 MUTATED DLC1 WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO            2            288
[1] 2 2
[1] FALSE

Clustering(10) Variable = ITGAL MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  ITGAL MUTATED     3   1
  ITGAL WILD-TYPE 383  12
  ITGAL MUTATED ITGAL WILD-TYPE 
              4             395 
  ITGAL MUTATED ITGAL WILD-TYPE 
              1              12 
$`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        18.21        16.34         8.25        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
       11.57        16.73         7.56        15.12        17.69        23.34 
TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T 
       20.71         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 
        5.10        17.52         1.22        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        15.48 
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         6.35 
TCGA-BJ-A45I TCGA-BJ-A45J TCGA-BJ-A45K TCGA-BJ-A4O8 TCGA-BJ-A4O9 TCGA-CE-A13K 
        6.18        21.63         8.98         4.93        23.47         0.53 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 TCGA-CE-A485 
        0.10         0.20         0.23        10.68         0.39         0.10 
TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DE-A4M8 
       20.22        15.42        36.46         5.98        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        17.26        14.07       169.32         3.39 
TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X 
        8.71        56.19        23.38        18.35        14.60         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        13.12         7.99        14.96 
TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
        7.20         1.45        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 
        7.99         5.33        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 
       12.56         8.28        34.85         5.52         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         9.44        37.48 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB 
       36.46        10.09         7.10        35.90        12.43        35.18 
TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP 
       15.88        15.09        31.04        20.45        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        24.23        17.69        59.57 
TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VE 
       11.34        21.37        23.21        24.82        22.92        18.97 
TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
        7.76        24.20        17.23        27.62        18.21        21.34 
TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 TCGA-DJ-A4V5 
       14.14        14.70        17.82         3.12        15.81        24.33 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 
       54.90        21.53         2.33        31.07        12.07        66.38 
TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 TCGA-E8-A2EA 
       40.21        63.19        30.31        14.04        31.23        22.29 
TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 TCGA-E8-A436 
       13.61        13.81         3.02        25.45        14.70        14.96 
TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN 
        7.69        13.78        13.58        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        80.91         4.18        58.82       139.86 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP 
       98.53        45.40        57.11       108.36        64.87         1.41 
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       131.15       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       130.72       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3TA TCGA-EL-A3TB 
       32.48        98.24        41.29       107.47        66.90        82.82 
TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZN TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZT 
       78.97        31.50        53.06        61.22        60.16        59.44 
TCGA-EL-A4JV TCGA-EL-A4JW TCGA-EL-A4JX TCGA-EL-A4JZ TCGA-EL-A4K0 TCGA-EL-A4K2 
       57.47        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        12.36        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-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N TCGA-EM-A22O TCGA-EM-A22P 
       15.75        10.45        14.53        10.65        11.74        11.15 
TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO 
       14.24        16.44        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        10.49        13.15        22.16 
TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 
       13.84        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-A3AP TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK 
       33.07         8.35        29.72        37.25        27.95        23.77 
TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO TCGA-EM-A3FP TCGA-EM-A3FQ 
       16.80        21.01        12.07        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        12.53         9.24 
TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A4FK TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ 
       13.91         7.82        21.34         5.33        26.37        22.45 
TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J 
       21.53        24.46        13.68        47.47        48.20        29.69 
TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 
       32.35        27.09        29.49        22.09        12.26        16.08 
TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K 
       29.19         2.66        58.22        13.74        71.01        80.02 
TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R 
       65.36        84.89        98.56        61.02        58.72        57.11 
TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ 
       55.10        59.15        28.24         5.85         4.18         2.43 
TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX 
        5.56        24.72        38.30        42.25         2.37         4.50 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT 
       80.81        69.24        59.87        43.50         0.30        17.98 
TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z 
       25.32       132.36        24.72         5.03         4.01        73.74 
TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 TCGA-FE-A234 TCGA-FE-A235 
       59.70        31.59        44.25        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        81.34        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        22.03         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 
       10.26        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         6.74        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 

  ITGAL MUTATED ITGAL WILD-TYPE 
           4.01            0.10 
  ITGAL MUTATED ITGAL WILD-TYPE 
         132.07          169.32 
  ITGAL MUTATED ITGAL WILD-TYPE 
           9.55           21.04 
[1] "4.0 - 132.1 (9.6)"  "0.1 - 169.3 (21.0)"
[1] "hr=" "6.8"
D10V2, 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     230       44        83        1        30         6
D10V3, multiclass
           clus
vv          ITGAL MUTATED ITGAL WILD-TYPE
  STAGE I               0             230
  STAGE II              1              44
  STAGE III             0              83
  STAGE IV              1               1
  STAGE IVA             2              30
  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 117 135 128  14
D10V4, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  T1             0             117
  T2             2             135
  T3             1             128
  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"
D10V5, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 188 167
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  188  167
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0             1             188
  1             3             167
[1] 2 2
[1] FALSE
D10V6, binary
                 cls
clus                0   1
  ITGAL MUTATED     2   0
  ITGAL WILD-TYPE 219   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      2    0
  ITGAL WILD-TYPE  219    7
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0             2             219
  1             0               7
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 297  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  297   99
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  FEMALE             1             297
  MALE               3              99
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  ITGAL MUTATED                0                                             4
  ITGAL WILD-TYPE              6                                           277
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  ITGAL MUTATED                                                                        0
  ITGAL WILD-TYPE                                                                     83
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  ITGAL MUTATED                                                                     0
  ITGAL WILD-TYPE                                                                  30
D10V8, 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                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      277
  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"
D10V9, binary
                 cls
clus                0   1
  ITGAL MUTATED     0   4
  ITGAL WILD-TYPE  12 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      0    4
  ITGAL WILD-TYPE   12  384
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO              0              12
  YES             4             384
[1] 2 2
[1] FALSE
D10V10, 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          103                      10  270                   0
D10V11, multiclass
                         clus
vv                        ITGAL MUTATED ITGAL WILD-TYPE
  MINIMAL (T3)                        0             103
  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 311  35   3  22
D10V12, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  R0             2             311
  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"
D10V13, continuous
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2             301 
     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-DE-A0XZ      TCGA-DE-A0Y2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DE-A0Y3      TCGA-DE-A3KN      TCGA-DE-A4M8      TCGA-DJ-A13M 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13O      TCGA-DJ-A13R      TCGA-DJ-A13T      TCGA-DJ-A13V 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A13W      TCGA-DJ-A13X      TCGA-DJ-A1QG      TCGA-DJ-A1QH 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A1QM      TCGA-DJ-A2PO      TCGA-DJ-A2PP      TCGA-DJ-A2PQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PR      TCGA-DJ-A2PS      TCGA-DJ-A2PT      TCGA-DJ-A2PU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PV      TCGA-DJ-A2PW      TCGA-DJ-A2PX      TCGA-DJ-A2PY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2PZ      TCGA-DJ-A2Q0      TCGA-DJ-A2Q1      TCGA-DJ-A2Q2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q3      TCGA-DJ-A2Q4      TCGA-DJ-A2Q5      TCGA-DJ-A2Q6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2Q7      TCGA-DJ-A2Q8      TCGA-DJ-A2Q9      TCGA-DJ-A2QA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A2QB      TCGA-DJ-A3UK      TCGA-DJ-A3UM      TCGA-DJ-A3UN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UO      TCGA-DJ-A3UP      TCGA-DJ-A3UQ      TCGA-DJ-A3UR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3UU      TCGA-DJ-A3UW      TCGA-DJ-A3UX      TCGA-DJ-A3V7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3VA      TCGA-DJ-A3VB      TCGA-DJ-A3VF      TCGA-DJ-A3VJ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A3VL      TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-DJ-A4V2      TCGA-DJ-A4V5      TCGA-DO-A1K0      TCGA-DO-A2HM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A242 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A2EA      TCGA-E8-A415      TCGA-E8-A419      TCGA-E8-A433 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-E8-A436      TCGA-E8-A44K      TCGA-EL-A3CM      TCGA-EL-A3CN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CO      TCGA-EL-A3CR      TCGA-EL-A3CS      TCGA-EL-A3CT 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CU      TCGA-EL-A3CV      TCGA-EL-A3CW      TCGA-EL-A3CX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3CY      TCGA-EL-A3CZ      TCGA-EL-A3D0      TCGA-EL-A3D1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3D4      TCGA-EL-A3D5      TCGA-EL-A3D6      TCGA-EL-A3GO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GP      TCGA-EL-A3GQ      TCGA-EL-A3GS      TCGA-EL-A3GU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3GV      TCGA-EL-A3GX      TCGA-EL-A3H3      TCGA-EL-A3H4 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3H5      TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3MX      TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3T0 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3TB      TCGA-EL-A3ZH 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A4JV      TCGA-EL-A4JW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EL-A4KI      TCGA-EM-A1CS      TCGA-EM-A1CT      TCGA-EM-A1CU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1CV      TCGA-EM-A1CW      TCGA-EM-A1YC      TCGA-EM-A1YD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22L      TCGA-EM-A22M      TCGA-EM-A22N      TCGA-EM-A22O 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A22P      TCGA-EM-A22Q      TCGA-EM-A2CK      TCGA-EM-A2CN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CP      TCGA-EM-A2CQ      TCGA-EM-A2CR      TCGA-EM-A2CT 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2CU      TCGA-EM-A2OV      TCGA-EM-A2OX      TCGA-EM-A2OY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A2OZ      TCGA-EM-A2P0      TCGA-EM-A2P1      TCGA-EM-A2P2 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AJ      TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3AQ      TCGA-EM-A3AR      TCGA-EM-A3FJ      TCGA-EM-A3FK 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FL      TCGA-EM-A3FM      TCGA-EM-A3FN      TCGA-EM-A3FO 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3FP      TCGA-EM-A3FQ      TCGA-EM-A3FR      TCGA-EM-A3O3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A3O8      TCGA-EM-A3O9      TCGA-EM-A3OA      TCGA-EM-A3OB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A4FM      TCGA-EM-A4FO      TCGA-EM-A4FQ      TCGA-EM-A4FR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-EM-A4FV      TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A25J      TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A2MZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4      TCGA-ET-A39K 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39L      TCGA-ET-A39O      TCGA-ET-A39P      TCGA-ET-A39R 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A39S      TCGA-ET-A39T      TCGA-ET-A3BO      TCGA-ET-A3BP 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BQ      TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3BV      TCGA-ET-A3BX      TCGA-ET-A3DQ      TCGA-ET-A3DR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-ET-A3DW      TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A230      TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PC      TCGA-FE-A3PD 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FK-A3S3      TCGA-FK-A3SB      TCGA-FK-A3SE      TCGA-FK-A3SG 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FK-A3SH      TCGA-FY-A2QD      TCGA-FY-A3I4      TCGA-FY-A3I5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3NM      TCGA-FY-A3NN      TCGA-FY-A3ON      TCGA-FY-A3R6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A3R7      TCGA-FY-A3R9      TCGA-FY-A3W9      TCGA-FY-A40K 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-FY-A4B3      TCGA-GE-A2C6      TCGA-H2-A26U      TCGA-H2-A2K9 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-H2-A3RH      TCGA-H2-A3RI      TCGA-H2-A421      TCGA-IM-A3EB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IM-A3ED      TCGA-IM-A3U2      TCGA-IM-A3U3      TCGA-J8-A3NZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-J8-A3O0      TCGA-J8-A3O1      TCGA-J8-A3YE      TCGA-J8-A4HW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-KS-A41J      TCGA-KS-A4I5      TCGA-KS-A4I9      TCGA-KS-A4IB 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L6-A4EP      TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-MK-A4N9 
"ITGAL WILD-TYPE" 
D10V14, binary
                 cls
clus                0   1
  ITGAL MUTATED     1   3
  ITGAL WILD-TYPE 180 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    3
  ITGAL WILD-TYPE  180  207
            clus
vv           ITGAL MUTATED ITGAL WILD-TYPE
  MULTIFOCAL             1             180
  UNIFOCAL               3             207
[1] 2 2
[1] FALSE
D10V15, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGAL MUTATED       0                         0     3
  ITGAL WILD-TYPE    38                        18   259
D10V16, multiclass
                           clus
vv                          ITGAL MUTATED ITGAL WILD-TYPE
  ASIAN                                 0              38
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             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
  ITGAL MUTATED     1   2
  ITGAL WILD-TYPE  30 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1    2
  ITGAL WILD-TYPE   30  288
                        clus
vv                       ITGAL MUTATED ITGAL WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO             2             288
[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  13
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             396 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              0              13 
$`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        18.21        16.34         8.25        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         7.56        15.12        17.69 
TCGA-BJ-A18Y TCGA-BJ-A18Z TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S 
       23.34        20.71         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         5.10        17.52         1.22        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 
       15.48        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 
        6.35         6.18        21.63         8.98         4.93        23.47 
TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A482 TCGA-CE-A484 
        0.53         0.10         0.20         0.23        10.68         0.39 
TCGA-CE-A485 TCGA-DE-A0XZ TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
        0.10        20.22        15.42        36.46         5.98        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        17.26        14.07       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        3.39         8.71        56.19        23.38        18.35        14.60 
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        13.12         7.99 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
       14.96         7.20         1.45        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         7.99         5.33        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        12.56         8.28        34.85         5.52         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         9.44 
TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA 
       37.48        36.46        10.09         7.10        35.90        12.43 
TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO 
       35.18        15.88        15.09        31.04        20.45        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        24.23        17.69 
TCGA-DJ-A3UW TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3V7 TCGA-DJ-A3VA TCGA-DJ-A3VB 
       59.57        11.34        21.37        23.21        24.82        22.92 
TCGA-DJ-A3VE TCGA-DJ-A3VF TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL 
       18.97         7.76        24.20        17.23        27.62        18.21 
TCGA-DJ-A4UP TCGA-DJ-A4UT TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V4 
       21.34        14.14        14.70        17.82         3.12        15.81 
TCGA-DJ-A4V5 TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-DO-A2HM TCGA-E3-A3DY TCGA-E3-A3DZ 
       24.33        54.90        21.53         2.33        31.07        12.07 
TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 TCGA-E8-A242 
       66.38        40.21        63.19        30.31        14.04        31.23 
TCGA-E8-A2EA TCGA-E8-A413 TCGA-E8-A415 TCGA-E8-A418 TCGA-E8-A419 TCGA-E8-A433 
       22.29        13.61        13.81         3.02        25.45        14.70 
TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM 
       14.96         7.69        13.78        13.58        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        80.91         4.18        58.82 
TCGA-EL-A3D0 TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D5 TCGA-EL-A3D6 TCGA-EL-A3GO 
      139.86        98.53        45.40        57.11       108.36        64.87 
TCGA-EL-A3GP TCGA-EL-A3GQ TCGA-EL-A3GR TCGA-EL-A3GS TCGA-EL-A3GU TCGA-EL-A3GV 
        1.41        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       131.15       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       130.72 
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        31.50        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 
       12.36        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        11.74        11.15        14.24        16.44        17.88 
TCGA-EM-A2CL TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR 
       13.18        23.51         6.05         2.99        12.30        13.64 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       10.49        13.15        22.16        13.84        19.73        32.32 
TCGA-EM-A2OZ TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI 
       33.96        17.59        17.46        17.29        14.60        22.52 
TCGA-EM-A3AJ TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP 
       30.94        15.68        14.14        33.07        13.38         8.35 
TCGA-EM-A3AQ TCGA-EM-A3AR TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM 
       29.72        37.25        27.95        23.77        16.80        21.01 
TCGA-EM-A3FN TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 
       12.07        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        12.53         9.24        13.91         7.82        21.34 
TCGA-EM-A4FM TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FV TCGA-EM-A4G1 
        5.33        26.37        22.45        21.53        24.46        13.68 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O TCGA-ET-A25R 
       47.47        48.20        29.69        32.35        27.09        29.49 
TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N4 TCGA-ET-A2N5 
       22.09        12.26        16.08        29.19         2.66        58.22 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L TCGA-ET-A39M TCGA-ET-A39N 
       13.74        71.01        80.02        65.36        84.89        98.56 
TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN 
       61.02        58.72        57.11        55.10        59.15        28.24 
TCGA-ET-A3BO TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU 
        5.85         4.18         2.43         5.56        24.72        38.30 
TCGA-ET-A3BV TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       42.25         2.37         4.50        80.81        69.24        59.87 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       43.50         0.30        17.98        25.32       132.36        24.72 
TCGA-ET-A40S TCGA-ET-A4KN TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 
        5.03         4.01        73.74        59.70        31.59        44.25 
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        81.34        81.83 
TCGA-FE-A3PB TCGA-FE-A3PD TCGA-FK-A3SB TCGA-FK-A3SD TCGA-FK-A3SE TCGA-FK-A3SG 
       85.15        78.77         4.11         1.05        22.03         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        10.26        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         6.74        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 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
          17.49            0.10 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          85.68          169.32 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          71.08           21.01 
[1] "17.5 - 85.7 (71.1)" "0.1 - 169.3 (21.0)"
[1] "hr="     "9200000"
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     227       45        83        2        32         6
D11V3, multiclass
           clus
vv          NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I               3             227
  STAGE II              0              45
  STAGE III             0              83
  STAGE IV              0               2
  STAGE IVA             0              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
  NLRP6 MUTATED     0   0   3   0
  NLRP6 WILD-TYPE 117 137 126  15
D11V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             0             117
  T2             0             137
  T3             3             126
  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 188 168
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE  188  168
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1             188
  1             2             168
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   0
  NLRP6 WILD-TYPE 221   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    0
  NLRP6 WILD-TYPE  221    7
D11V7, binary
                 cls
clus                0   1
  NLRP6 MUTATED     2   1
  NLRP6 WILD-TYPE 296 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  296  101
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             2             296
  MALE               1             101
[1] 2 2
[1] FALSE
                 vv
clus              OTHER  SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  NLRP6 MUTATED                0                                             2
  NLRP6 WILD-TYPE              6                                           279
                 vv
clus              THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  NLRP6 MUTATED                                                                        1
  NLRP6 WILD-TYPE                                                                     82
                 vv
clus              THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  NLRP6 MUTATED                                                                     0
  NLRP6 WILD-TYPE                                                                  30
D11V8, 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                                                                       6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      279
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              82
  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"
D11V9, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   3
  NLRP6 WILD-TYPE  12 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    3
  NLRP6 WILD-TYPE   12  385
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              0              12
  YES             3             385
[1] 2 2
[1] FALSE
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          102                      11  270                   1
D11V11, multiclass
                         clus
vv                        NLRP6 MUTATED NLRP6 WILD-TYPE
  MINIMAL (T3)                        1             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
  NLRP6 MUTATED     3   0   0   0
  NLRP6 WILD-TYPE 310  37   3  22
D11V12, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             3             310
  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 179 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE  179  209
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  MULTIFOCAL             2             179
  UNIFOCAL               1             209
[1] 2 2
[1] FALSE
D11V15, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             324 
     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-A3VL      TCGA-DJ-A3VM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4UL      TCGA-DJ-A4UP      TCGA-DJ-A4UT      TCGA-DJ-A4V0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V2      TCGA-DJ-A4V4      TCGA-DJ-A4V5      TCGA-DO-A1JZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DO-A1K0      TCGA-DO-A2HM      TCGA-E3-A3DY      TCGA-E3-A3DZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E0      TCGA-E3-A3E1      TCGA-E3-A3E2      TCGA-E3-A3E3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A419      TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H2      TCGA-EL-A3H3      TCGA-EL-A3H4      TCGA-EL-A3H5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H7      TCGA-EL-A3H8      TCGA-EL-A3MW      TCGA-EL-A3MX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3MY      TCGA-EL-A3MZ      TCGA-EL-A3N2      TCGA-EL-A3N3 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T1      TCGA-EL-A3T2      TCGA-EL-A3T3      TCGA-EL-A3T6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T7      TCGA-EL-A3T8      TCGA-EL-A3T9      TCGA-EL-A3TA 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3TB      TCGA-EL-A3ZH      TCGA-EL-A3ZK      TCGA-EL-A3ZN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZQ      TCGA-EL-A3ZR      TCGA-EL-A3ZT      TCGA-EL-A4JV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JW      TCGA-EL-A4JX      TCGA-EL-A4JZ      TCGA-EL-A4K0 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K2      TCGA-EL-A4K4      TCGA-EL-A4K6      TCGA-EL-A4KD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KG      TCGA-EL-A4KH      TCGA-EL-A4KI      TCGA-EM-A1CS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1CT      TCGA-EM-A1CU      TCGA-EM-A1CV      TCGA-EM-A1CW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YA      TCGA-EM-A1YB      TCGA-EM-A1YC      TCGA-EM-A1YD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A1YE      TCGA-EM-A22I      TCGA-EM-A22J      TCGA-EM-A22K 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22L      TCGA-EM-A22N      TCGA-EM-A22O      TCGA-EM-A22P 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A22Q      TCGA-EM-A2CJ      TCGA-EM-A2CK      TCGA-EM-A2CL 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CN      TCGA-EM-A2CO      TCGA-EM-A2CP      TCGA-EM-A2CQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2CR      TCGA-EM-A2CT      TCGA-EM-A2CU      TCGA-EM-A2OW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2OX      TCGA-EM-A2OY      TCGA-EM-A2P0      TCGA-EM-A2P1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A2P2      TCGA-EM-A2P3      TCGA-EM-A3AI      TCGA-EM-A3AJ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AK      TCGA-EM-A3AL      TCGA-EM-A3AN      TCGA-EM-A3AO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AP      TCGA-EM-A3AQ      TCGA-EM-A3AR      TCGA-EM-A3FJ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3FM      TCGA-EM-A3FN      TCGA-EM-A3FP      TCGA-EM-A3FR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3O3      TCGA-EM-A3O6      TCGA-EM-A3O7      TCGA-EM-A3O8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3O9      TCGA-EM-A3OA      TCGA-EM-A3OB      TCGA-EM-A4FK 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A4FM      TCGA-EM-A4FQ      TCGA-EM-A4FR      TCGA-EM-A4FV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A4G1      TCGA-ET-A25G      TCGA-ET-A25I      TCGA-ET-A25J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A25R      TCGA-ET-A2MY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N5      TCGA-ET-A39J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39O      TCGA-ET-A39P 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39T      TCGA-ET-A3BN      TCGA-ET-A3BO      TCGA-ET-A3BP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BQ      TCGA-ET-A3BS      TCGA-ET-A3BT      TCGA-ET-A3BU 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BV      TCGA-ET-A3BW      TCGA-ET-A3BX      TCGA-ET-A3DO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DS      TCGA-ET-A3DT      TCGA-ET-A40S      TCGA-ET-A4KN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A22Z      TCGA-FE-A230      TCGA-FE-A232      TCGA-FE-A233 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A234      TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A23A      TCGA-FE-A3PB      TCGA-FE-A3PD      TCGA-FY-A2QD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3ON      TCGA-FY-A3R8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3W9      TCGA-FY-A40K      TCGA-FY-A4B3      TCGA-GE-A2C6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED      TCGA-IM-A3U2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3U3      TCGA-J8-A3O0      TCGA-KS-A41J      TCGA-KS-A4I5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP      TCGA-L6-A4ET 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED       0                         1     1
  NLRP6 WILD-TYPE    38                        17   261
D11V16, multiclass
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             316 
     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-A3VL      TCGA-DJ-A3VM      TCGA-DJ-A4UL      TCGA-DJ-A4UP 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4UT      TCGA-DJ-A4UW      TCGA-DJ-A4V0      TCGA-DJ-A4V4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-DJ-A4V5      TCGA-DO-A1JZ      TCGA-DO-A1K0      TCGA-DO-A2HM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3DY      TCGA-E3-A3DZ      TCGA-E3-A3E0      TCGA-E3-A3E1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E3-A3E2      TCGA-E3-A3E3      TCGA-E3-A3E5      TCGA-E8-A242 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A2EA      TCGA-E8-A413      TCGA-E8-A415      TCGA-E8-A418 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A419      TCGA-E8-A433      TCGA-E8-A436      TCGA-E8-A437 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-E8-A44K      TCGA-E8-A44M      TCGA-EL-A3CL      TCGA-EL-A3CM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CN      TCGA-EL-A3CO      TCGA-EL-A3CP      TCGA-EL-A3CR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CS      TCGA-EL-A3CT      TCGA-EL-A3CU      TCGA-EL-A3CV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3CW      TCGA-EL-A3CX      TCGA-EL-A3CY      TCGA-EL-A3CZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D0      TCGA-EL-A3D1      TCGA-EL-A3D4      TCGA-EL-A3D5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3D6      TCGA-EL-A3GO      TCGA-EL-A3GP      TCGA-EL-A3GQ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GR      TCGA-EL-A3GS      TCGA-EL-A3GU      TCGA-EL-A3GV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3GW      TCGA-EL-A3GX      TCGA-EL-A3GY      TCGA-EL-A3GZ 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3H1      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-A3T0      TCGA-EL-A3T1      TCGA-EL-A3T2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T3      TCGA-EL-A3T6      TCGA-EL-A3T7      TCGA-EL-A3T8 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3T9      TCGA-EL-A3TA      TCGA-EL-A3TB      TCGA-EL-A3ZH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZK      TCGA-EL-A3ZN      TCGA-EL-A3ZQ      TCGA-EL-A3ZR 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A3ZT      TCGA-EL-A4JV      TCGA-EL-A4JW      TCGA-EL-A4JX 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4JZ      TCGA-EL-A4K0      TCGA-EL-A4K2      TCGA-EL-A4K4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4K6      TCGA-EL-A4KD      TCGA-EL-A4KG      TCGA-EL-A4KH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EL-A4KI      TCGA-EM-A22M      TCGA-EM-A22O      TCGA-EM-A2OV 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-EM-A3AI      TCGA-ET-A25G      TCGA-ET-A25I      TCGA-ET-A25J 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A25K      TCGA-ET-A25O      TCGA-ET-A25R      TCGA-ET-A2MY 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2MZ      TCGA-ET-A2N0      TCGA-ET-A2N1      TCGA-ET-A2N4 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A2N5      TCGA-ET-A39I      TCGA-ET-A39J      TCGA-ET-A39K 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39M      TCGA-ET-A39N      TCGA-ET-A39O      TCGA-ET-A39P 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A39R      TCGA-ET-A39S      TCGA-ET-A39T      TCGA-ET-A3BN 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3BO      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-A3DO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DP      TCGA-ET-A3DQ      TCGA-ET-A3DR      TCGA-ET-A3DS 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A3DT      TCGA-ET-A3DU      TCGA-ET-A3DV      TCGA-ET-A3DW 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-ET-A40S      TCGA-ET-A4KN      TCGA-FE-A22Z      TCGA-FE-A230 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A231      TCGA-FE-A232      TCGA-FE-A233      TCGA-FE-A234 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A235      TCGA-FE-A236      TCGA-FE-A237      TCGA-FE-A23A 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FE-A3PB      TCGA-FE-A3PD      TCGA-FK-A3SB      TCGA-FK-A3SD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FK-A3SE      TCGA-FK-A3SG      TCGA-FK-A3SH      TCGA-FY-A2QD 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3BL      TCGA-FY-A3I4      TCGA-FY-A3I5      TCGA-FY-A3NM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3NP      TCGA-FY-A3ON      TCGA-FY-A3R6      TCGA-FY-A3R7 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3R8      TCGA-FY-A3R9      TCGA-FY-A3RA      TCGA-FY-A3W9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-FY-A3WA      TCGA-FY-A40K      TCGA-FY-A4B3      TCGA-GE-A2C6 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H2-A26U      TCGA-H2-A2K9      TCGA-H2-A3RH      TCGA-H2-A3RI 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-H2-A421      TCGA-IM-A3EB      TCGA-IM-A3ED      TCGA-IM-A3U2 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IM-A3U3      TCGA-J8-A3NZ      TCGA-J8-A3O0      TCGA-J8-A3O1 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-J8-A3YE      TCGA-J8-A4HW      TCGA-KS-A41J      TCGA-KS-A4I5 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-KS-A4I9      TCGA-KS-A4IB      TCGA-L6-A4EP      TCGA-L6-A4ET 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-L6-A4EU      TCGA-MK-A4N6      TCGA-MK-A4N7      TCGA-MK-A4N9 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
D11V17, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   2
  NLRP6 WILD-TYPE  31 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    2
  NLRP6 WILD-TYPE   31  288
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             2             288
[1] 2 2
[1] FALSE
