[1] "ofn"        "-oTTHCA-TP"
[1] "opt"       "-OPAPOBEC"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "APOBEC"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/22507188/THCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/THCA-TP/22507680/APOBEC_clinical_corr_input_22537043/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=503, in cluster file=496, common to both=492
[1]   2 492
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 472   10   10 
   0 HIGH  LOW 
 472   10   10 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH   FC.NO.ENRICH 
            20            472 
FC.HIGH.ENRICH   FC.NO.ENRICH 
            20            472 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RADIATION_EXPOSURE"                  
[15] "EXTRATHYROIDAL_EXTENSION"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "MULTIFOCALITY"                       
[19] "TUMOR_SIZE"                          
[20] "RACE"                                
[21] "ETHNICITY"                           

Input Data has 21 rows and 492 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=72,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=431,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATION_EXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXTRATHYROIDAL_EXTENSION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'MULTIFOCALITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_SIZE':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 492 columns, 1 survival variables, and 16 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"           "PATHOLOGIC_STAGE"        
 [3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
 [5] "PATHOLOGY_M_STAGE"        "GENDER"                  
 [7] "RADIATION_THERAPY"        "HISTOLOGICAL_TYPE"       
 [9] "RADIATION_EXPOSURE"       "EXTRATHYROIDAL_EXTENSION"
[11] "RESIDUAL_TUMOR"           "NUMBER_OF_LYMPH_NODES"   
[13] "MULTIFOCALITY"            "TUMOR_SIZE"              
[15] "RACE"                     "ETHNICITY"               
YEARS_TO_BIRTH, nv=72, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
141 162 164  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
141 162 164  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
141 162 164  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
141 162 164  23 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_EXPOSURE, nv=2, binary=FALSE, numeric=FALSE
EXTRATHYROIDAL_EXTENSION, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=29, binary=FALSE, numeric=TRUE
MULTIFOCALITY, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SIZE, nv=61, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2    0   1
  0    458  13
  HIGH   9   1
  LOW   10   0
   0 HIGH  LOW 
 471   10   10 
   0 HIGH  LOW 
  13    1    0 
$`0`
TCGA-BJ-A290 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3UU 
       30.21        23.18        12.66        35.84        27.45        23.44 
TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3CR 
       59.57        42.54         3.12        24.76        39.95         7.66 
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ TCGA-EL-A3H2 
       45.53         4.18       139.86        57.11        50.24        33.50 
TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV 
      150.48        17.52       178.29        29.72        50.40        75.42 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       11.57        16.73        25.48        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28X TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       30.97        18.38        16.57        20.48        12.82        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E 
       13.94        36.39        23.31        18.64        10.88        21.01 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        3.45        23.84        28.44        15.45        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       33.04        34.78        26.93        35.54         3.12        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       63.19        52.44        31.23        35.67        11.70        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
      158.83       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       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-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        65.49        61.22        60.16         7.07 
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        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       48.49        18.05        19.79        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CS 
       23.51         6.05         2.99        12.30        13.64        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
       13.68        81.93        81.70        77.56        70.42        65.29 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PA 
       68.22       117.40        66.77       112.80        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        7.82        29.10        16.14        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       16.90        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 TCGA-MK-A4N7 
       35.28        33.24        33.40        40.37        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

$HIGH
TCGA-4C-A93U TCGA-BJ-A2NA TCGA-DJ-A4UT TCGA-DO-A2HM TCGA-EL-A3CT TCGA-EL-A3ZO 
        4.24        18.97        27.06         2.33        60.95        72.69 
TCGA-EL-A4KG TCGA-ET-A2MY TCGA-IM-A41Y TCGA-L6-A4EU 
       24.30        58.75        21.83         9.50 

$LOW
TCGA-DJ-A13L TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A28Z TCGA-BJ-A45J TCGA-DJ-A1QM 
        9.96         4.01        15.12        11.08        21.63         6.02 
TCGA-DJ-A4V4 TCGA-EM-A1YB TCGA-EM-A2OZ TCGA-EM-A3SX 
       15.81        19.46        33.96        29.85 

   0 HIGH  LOW 
0.20 2.33 4.01 
     0   HIGH    LOW 
178.29  72.69  33.96 
     0   HIGH    LOW 
31.400 23.065 15.465 
[1] "0.2 - 178.3 (31.4)" "2.3 - 72.7 (23.1)"  "4.0 - 34.0 (15.5)" 
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  0        268       49       104        2        41         6
  HIGH       4        0         3        0         3         0
  LOW        6        1         1        0         2         0
D1V3, multiclass
           clus
vv            0 HIGH LOW
  STAGE I   268    4   6
  STAGE II   49    0   1
  STAGE III 104    3   1
  STAGE IV    2    0   0
  STAGE IVA  41    3   2
  STAGE IVC   6    0   0
[1] 6 3
[1] 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
  0    133 160 156  21
  HIGH   3   0   5   2
  LOW    5   2   3   0
D1V4, multiclass
    clus
vv     0 HIGH LOW
  T1 133    3   5
  T2 160    0   2
  T3 156    5   3
  T4  21    2   0
[1] 4 3
[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
  0    213 211
  HIGH   3   6
  LOW    4   5
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     213  211
  HIGH    3    6
  LOW     4    5
   clus
vv    0 HIGH LOW
  0 213    3   4
  1 211    6   5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus     0   1
  0    263   9
  HIGH   7   0
  LOW    6   0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     263    9
  HIGH    7    0
  LOW     6    0
   clus
vv    0 HIGH LOW
  0 263    7   6
  1   9    0   0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
      cls
clus     0   1
  0    348 124
  HIGH   8   2
  LOW    6   4
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     348  124
  HIGH    8    2
  LOW     6    4
        clus
vv         0 HIGH LOW
  FEMALE 348    8   6
  MALE   124    2   4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
      cls
clus     0   1
  0    168 290
  HIGH   6   3
  LOW    5   5
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     168  290
  HIGH    6    3
  LOW     5    5
     clus
vv      0 HIGH LOW
  NO  168    6   5
  YES 290    3   5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  0                 6                                           336
  HIGH              1                                             8
  LOW               0                                             4
      vv
clus   THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  0                                                                       100
  HIGH                                                                      0
  LOW                                                                       2
      vv
clus   THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  0                                                                     30
  HIGH                                                                   1
  LOW                                                                    4
D1V9, multiclass
                                                                        clus
vv                                                                         0
  OTHER, SPECIFY                                                           6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                          336
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)     30
                                                                        clus
vv                                                                       HIGH
  OTHER, SPECIFY                                                            1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                             8
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)    0
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)       1
                                                                        clus
vv                                                                       LOW
  OTHER, SPECIFY                                                           0
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                            4
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)   2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)      4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
      cls
clus     0   1
  0    401  15
  HIGH   8   0
  LOW    6   2
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     401   15
  HIGH    8    0
  LOW     6    2
     clus
vv      0 HIGH LOW
  NO  401    8   6
  YES  15    0   2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  0             124                      15  318                   1
  HIGH            5                       2    3                   0
  LOW             1                       1    7                   0
D1V11, multiclass
                         clus
vv                          0 HIGH LOW
  MINIMAL (T3)            124    5   1
  MODERATE/ADVANCED (T4A)  15    2   1
  NONE                    318    3   7
  VERY ADVANCED (T4B)       1    0   0
[1] 4 3
[1] 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
  0    367  47   4  28
  HIGH   7   2   0   1
  LOW    5   2   0   1
D1V12, multiclass
    clus
vv     0 HIGH LOW
  R0 367    7   5
  R1  47    2   2
  R2   4    0   0
  RX  28    1   1
[1] 4 3
[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
  0    210 255
  HIGH   4   6
  LOW    7   1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     210  255
  HIGH    4    6
  LOW     7    1
            clus
vv             0 HIGH LOW
  MULTIFOCAL 210    4   7
  UNIFOCAL   255    6   1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1    51                        23   308
  HIGH                                0     0                         3     7
  LOW                                 0     0                         0     7
D1V16, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   0
  ASIAN                             51    0   0
  BLACK OR AFRICAN AMERICAN         23    3   0
  WHITE                            308    7   7
[1] 4 3
[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
  0     37 335
  HIGH   1   9
  LOW    0   7
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      37  335
  HIGH    1    9
  LOW     0    7
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      37    1   0
  NOT HISPANIC OR LATINO 335    9   7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH  19   1
  FC.NO.ENRICH   458  13
FC.HIGH.ENRICH   FC.NO.ENRICH 
            20            471 
FC.HIGH.ENRICH   FC.NO.ENRICH 
             1             13 
$FC.HIGH.ENRICH
TCGA-DJ-A13L TCGA-4C-A93U TCGA-BJ-A0ZB TCGA-BJ-A0ZH TCGA-BJ-A28Z TCGA-BJ-A2NA 
        9.96         4.24         4.01        15.12        11.08        18.97 
TCGA-BJ-A45J TCGA-DJ-A1QM TCGA-DJ-A4UT TCGA-DJ-A4V4 TCGA-DO-A2HM TCGA-EL-A3CT 
       21.63         6.02        27.06        15.81         2.33        60.95 
TCGA-EL-A3ZO TCGA-EL-A4KG TCGA-EM-A1YB TCGA-EM-A2OZ TCGA-EM-A3SX TCGA-ET-A2MY 
       72.69        24.30        19.46        33.96        29.85        58.75 
TCGA-IM-A41Y TCGA-L6-A4EU 
       21.83         9.50 

$FC.NO.ENRICH
TCGA-BJ-A290 TCGA-BJ-A45K TCGA-CE-A13K TCGA-DE-A0XZ TCGA-DJ-A2PR TCGA-DJ-A3UU 
       30.21        23.18        12.66        35.84        27.45        23.44 
TCGA-DJ-A3UW TCGA-DJ-A3V4 TCGA-DJ-A3VI TCGA-DJ-A3VK TCGA-E3-A3E5 TCGA-EL-A3CR 
       59.57        42.54         3.12        24.76        39.95         7.66 
TCGA-EL-A3CS TCGA-EL-A3CY TCGA-EL-A3D0 TCGA-EL-A3D5 TCGA-EL-A3GQ TCGA-EL-A3H2 
       45.53         4.18       139.86        57.11        50.24        33.50 
TCGA-EL-A3H8 TCGA-EL-A3MY TCGA-EL-A3N3 TCGA-EM-A3AQ TCGA-ET-A3BO TCGA-ET-A3BV 
      150.48        17.52       178.29        29.72        50.40        75.42 
TCGA-FK-A3SD TCGA-FY-A76V TCGA-J8-A3NZ TCGA-J8-A4HW TCGA-L6-A4ET TCGA-MK-A84Z 
        1.05         1.68        17.23         2.60        21.83        23.93 
TCGA-BJ-A0YZ TCGA-BJ-A0Z0 TCGA-BJ-A0Z2 TCGA-BJ-A0Z3 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA 
       24.79        13.78        49.78        16.34        41.33        18.87 
TCGA-BJ-A0ZC TCGA-BJ-A0ZE TCGA-BJ-A0ZG TCGA-BJ-A0ZJ TCGA-BJ-A18Y TCGA-BJ-A18Z 
       11.57        16.73        25.48        42.08        51.39        41.52 
TCGA-BJ-A191 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28S TCGA-BJ-A28T TCGA-BJ-A28V 
        4.83        44.35        42.15        21.04        35.54        32.45 
TCGA-BJ-A28X TCGA-BJ-A2N7 TCGA-BJ-A2N8 TCGA-BJ-A2N9 TCGA-BJ-A2P4 TCGA-BJ-A3EZ 
       30.97        18.38        16.57        20.48        12.82        16.01 
TCGA-BJ-A3F0 TCGA-BJ-A3PR TCGA-BJ-A3PT TCGA-BJ-A3PU TCGA-BJ-A45D TCGA-BJ-A45E 
       13.94        36.39        23.31        18.64        10.88        21.01 
TCGA-BJ-A45F TCGA-BJ-A45G TCGA-BJ-A45H TCGA-BJ-A45I TCGA-BJ-A4O8 TCGA-BJ-A4O9 
        3.45        23.84        28.44        15.45        19.43        23.47 
TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-CE-A481 TCGA-CE-A482 TCGA-CE-A483 
       12.30        12.79        12.46        11.38        10.68        15.02 
TCGA-CE-A484 TCGA-CE-A485 TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN 
       12.43        12.66        21.63        50.17        37.64        27.32 
TCGA-DE-A4M8 TCGA-DE-A4M9 TCGA-DE-A4MA TCGA-DE-A4MB TCGA-DE-A4MC TCGA-DE-A4MD 
       18.54        18.84        30.12        11.57        30.02        25.12 
TCGA-DE-A69J TCGA-DE-A69K TCGA-DE-A7U5 TCGA-DJ-A13M TCGA-DJ-A13O TCGA-DJ-A13P 
       14.70        14.27         2.76        48.79        38.17       169.32 
TCGA-DJ-A13R TCGA-DJ-A13S TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
       18.58         8.71        56.19        52.27        43.17        52.37 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
        8.32        48.07       135.91        30.61        44.98        42.51 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PN 
       14.96        17.59        42.58        47.41        17.56        10.09 
TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PS TCGA-DJ-A2PT TCGA-DJ-A2PU 
        7.99        30.58        35.41        26.20        38.83        33.96 
TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ TCGA-DJ-A2Q0 
       31.99        34.85        28.96         8.78         8.42        34.36 
TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q6 
       37.74        43.96        40.24        33.93        37.48        36.46 
TCGA-DJ-A2Q7 TCGA-DJ-A2Q8 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
       35.11        39.09        35.90        33.53        35.18        39.95 
TCGA-DJ-A3UK TCGA-DJ-A3UM TCGA-DJ-A3UN TCGA-DJ-A3UO TCGA-DJ-A3UP TCGA-DJ-A3UQ 
       36.92        31.04        32.42        31.46        16.41        19.56 
TCGA-DJ-A3UR TCGA-DJ-A3US TCGA-DJ-A3UT TCGA-DJ-A3UX TCGA-DJ-A3UY TCGA-DJ-A3UZ 
       36.33        32.81        36.33        11.34        35.87        40.96 
TCGA-DJ-A3V0 TCGA-DJ-A3V2 TCGA-DJ-A3V3 TCGA-DJ-A3V5 TCGA-DJ-A3V7 TCGA-DJ-A3V8 
       36.99        20.22        30.61        19.20        23.21        21.27 
TCGA-DJ-A3V9 TCGA-DJ-A3VA TCGA-DJ-A3VB TCGA-DJ-A3VD TCGA-DJ-A3VE TCGA-DJ-A3VF 
       20.48        24.82        22.92        40.70        18.97         9.60 
TCGA-DJ-A3VG TCGA-DJ-A3VJ TCGA-DJ-A3VL TCGA-DJ-A3VM TCGA-DJ-A4UL TCGA-DJ-A4UP 
       35.67        36.43        23.44        27.62        30.87        30.12 
TCGA-DJ-A4UQ TCGA-DJ-A4UR TCGA-DJ-A4UW TCGA-DJ-A4V0 TCGA-DJ-A4V2 TCGA-DJ-A4V5 
       33.04        34.78        26.93        35.54         3.12        35.38 
TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 
       54.90        21.53        92.55        47.21        66.38        80.52 
TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E8-A242 TCGA-E8-A2EA TCGA-E8-A2JQ TCGA-E8-A3X7 
       63.19        52.44        31.23        35.67        11.70        31.27 
TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A419 
       29.98        31.50        31.04        31.30        30.84        25.45 
TCGA-E8-A432 TCGA-E8-A433 TCGA-E8-A434 TCGA-E8-A436 TCGA-E8-A437 TCGA-E8-A438 
       30.61        31.27        31.33        14.96        39.88        33.50 
TCGA-E8-A44K TCGA-E8-A44M TCGA-EL-A3CL TCGA-EL-A3CM TCGA-EL-A3CN TCGA-EL-A3CO 
       31.00        30.15        31.66        26.73       155.54        97.74 
TCGA-EL-A3CP TCGA-EL-A3CU TCGA-EL-A3CV TCGA-EL-A3CW TCGA-EL-A3CX TCGA-EL-A3CZ 
      158.83       157.15        37.94        57.01       106.62        79.50 
TCGA-EL-A3D1 TCGA-EL-A3D4 TCGA-EL-A3D6 TCGA-EL-A3GO TCGA-EL-A3GP TCGA-EL-A3GR 
       98.53        69.57       108.36        64.87        49.51       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-A3H3 TCGA-EL-A3H4 TCGA-EL-A3H5 TCGA-EL-A3H7 
      139.99        49.32        43.36        49.71        83.57       139.00 
TCGA-EL-A3MW TCGA-EL-A3MX TCGA-EL-A3MZ TCGA-EL-A3N2 TCGA-EL-A3T0 TCGA-EL-A3T1 
      108.66        57.63        52.50        29.65       142.52       129.57 
TCGA-EL-A3T2 TCGA-EL-A3T3 TCGA-EL-A3T6 TCGA-EL-A3T7 TCGA-EL-A3T8 TCGA-EL-A3T9 
       32.48       132.07        98.24        41.29       107.47         5.72 
TCGA-EL-A3TA TCGA-EL-A3TB TCGA-EL-A3ZG TCGA-EL-A3ZH TCGA-EL-A3ZK TCGA-EL-A3ZL 
       66.90        82.82        89.56        91.17        51.78        62.30 
TCGA-EL-A3ZM TCGA-EL-A3ZN TCGA-EL-A3ZP TCGA-EL-A3ZQ TCGA-EL-A3ZR TCGA-EL-A3ZS 
       36.03        53.06        65.49        61.22        60.16         7.07 
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        61.02        31.04 
TCGA-EL-A4K1 TCGA-EL-A4K2 TCGA-EL-A4K4 TCGA-EL-A4K6 TCGA-EL-A4K7 TCGA-EL-A4K9 
       34.39        30.51        53.36        44.15        41.13        47.84 
TCGA-EL-A4KD TCGA-EL-A4KH TCGA-EL-A4KI TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
       43.59        27.06        23.90        26.86        18.18        20.91 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE 
       48.49        18.05        19.79        78.61        57.01        54.08 
TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22M TCGA-EM-A22N 
       14.73        14.50        15.75        10.45        14.53        10.65 
TCGA-EM-A22O TCGA-EM-A22P TCGA-EM-A22Q TCGA-EM-A2CJ TCGA-EM-A2CK TCGA-EM-A2CL 
       44.19        41.29        14.24        47.57        17.88        13.18 
TCGA-EM-A2CN TCGA-EM-A2CO TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CR TCGA-EM-A2CS 
       23.51         6.05         2.99        12.30        13.64        27.65 
TCGA-EM-A2CT TCGA-EM-A2CU TCGA-EM-A2OV TCGA-EM-A2OW TCGA-EM-A2OX TCGA-EM-A2OY 
       48.46        13.15        22.16        40.34        19.73        32.32 
TCGA-EM-A2P0 TCGA-EM-A2P1 TCGA-EM-A2P2 TCGA-EM-A2P3 TCGA-EM-A3AI TCGA-EM-A3AJ 
       17.59        17.46        17.29        14.60        22.52        30.94 
TCGA-EM-A3AK TCGA-EM-A3AL TCGA-EM-A3AN TCGA-EM-A3AO TCGA-EM-A3AP TCGA-EM-A3AR 
       15.68        14.14        33.07        44.52         8.35        37.25 
TCGA-EM-A3FJ TCGA-EM-A3FK TCGA-EM-A3FL TCGA-EM-A3FM TCGA-EM-A3FN TCGA-EM-A3FO 
       27.95        23.77        47.38        21.01        12.07        17.49 
TCGA-EM-A3FP TCGA-EM-A3FQ TCGA-EM-A3FR TCGA-EM-A3O3 TCGA-EM-A3O6 TCGA-EM-A3O7 
       17.39        16.18        15.02        14.50        15.06         7.33 
TCGA-EM-A3O8 TCGA-EM-A3O9 TCGA-EM-A3OA TCGA-EM-A3OB TCGA-EM-A3ST TCGA-EM-A3SU 
       12.53         9.24        27.02        38.66        38.86        29.95 
TCGA-EM-A3SY TCGA-EM-A3SZ TCGA-EM-A4FF TCGA-EM-A4FH TCGA-EM-A4FK TCGA-EM-A4FM 
       13.51        12.79        84.59        29.33        21.34         5.33 
TCGA-EM-A4FN TCGA-EM-A4FO TCGA-EM-A4FQ TCGA-EM-A4FR TCGA-EM-A4FU TCGA-EM-A4FV 
       26.37        26.37        22.45        21.53        60.49        24.46 
TCGA-EM-A4G1 TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25O 
       13.68        81.93        81.70        77.56        70.42        65.29 
TCGA-ET-A25R TCGA-ET-A2MX TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N1 TCGA-ET-A2N3 
       63.45        88.41        37.25        52.60        54.35        83.34 
TCGA-ET-A2N4 TCGA-ET-A2N5 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39K TCGA-ET-A39L 
        2.66        80.88        33.24       106.09       107.41       108.46 
TCGA-ET-A39M TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P TCGA-ET-A39R TCGA-ET-A39S 
       84.89       123.32       100.57        95.34        94.13        55.10 
TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BP TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT 
       98.20        28.24        79.10        76.64         5.79        87.62 
TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ 
       77.82        46.65        52.47       116.78        94.59        84.85 
TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DT TCGA-ET-A3DU TCGA-ET-A3DV TCGA-ET-A3DW 
       80.58        66.84        43.73        62.83       166.62        24.72 
TCGA-ET-A40P TCGA-ET-A40Q TCGA-ET-A40R TCGA-ET-A40S TCGA-ET-A40T TCGA-ET-A4KN 
       43.99        46.26        44.38        40.21        37.48        33.17 
TCGA-ET-A4KQ TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A232 TCGA-FE-A233 
       31.40        73.74        71.44        31.59        79.69        24.69 
TCGA-FE-A234 TCGA-FE-A235 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A23A TCGA-FE-A3PA 
       68.22       117.40        66.77       112.80        81.83       106.36 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FK-A3S3 TCGA-FK-A3SB TCGA-FK-A3SE 
       85.15        85.68        78.77        71.08         4.11        22.03 
TCGA-FK-A3SG TCGA-FK-A3SH TCGA-FK-A4UB TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I4 
        0.92        48.10       116.09         1.25        20.42        17.82 
TCGA-FY-A3I5 TCGA-FY-A3NM TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
        7.82        29.10        16.14        19.56        13.91        16.27 
TCGA-FY-A3R8 TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-FY-A3TY TCGA-FY-A3W9 TCGA-FY-A3WA 
       15.68        16.57        18.08        23.31        21.63        17.06 
TCGA-FY-A3YR TCGA-FY-A40K TCGA-FY-A40L TCGA-FY-A40M TCGA-FY-A40N TCGA-FY-A4B0 
       17.36        15.16        23.87        22.49        19.04        13.81 
TCGA-FY-A4B3 TCGA-FY-A4B4 TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
       14.04        21.60        12.53        17.00        21.67        12.46 
TCGA-H2-A3RI TCGA-H2-A421 TCGA-H2-A422 TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 
       11.01        20.05        18.61        48.92        47.41        18.51 
TCGA-IM-A3U3 TCGA-IM-A41Z TCGA-IM-A420 TCGA-IM-A4EB TCGA-J8-A3O0 TCGA-J8-A3O1 
       16.90        31.10         8.22        25.64        43.17        27.19 
TCGA-J8-A3O2 TCGA-J8-A3YD TCGA-J8-A3YE TCGA-J8-A3YF TCGA-J8-A3YG TCGA-J8-A3YH 
       11.24        31.82        27.85        24.69        22.29         5.75 
TCGA-J8-A42S TCGA-J8-A4HY TCGA-KS-A41F TCGA-KS-A41I TCGA-KS-A41J TCGA-KS-A41L 
        2.47         0.20       143.57        15.98        15.68       113.85 
TCGA-KS-A4I1 TCGA-KS-A4I3 TCGA-KS-A4I5 TCGA-KS-A4I7 TCGA-KS-A4I9 TCGA-KS-A4IB 
       26.70        43.69        18.64        32.45        87.39        84.72 
TCGA-KS-A4IC TCGA-KS-A4ID TCGA-L6-A4EP TCGA-L6-A4EQ TCGA-MK-A4N6 TCGA-MK-A4N7 
       35.28        33.24        33.40        40.37        36.10        32.45 
TCGA-MK-A4N9 TCGA-QD-A8IV TCGA-E8-A418 
       30.21        12.89         3.02 

FC.HIGH.ENRICH   FC.NO.ENRICH 
          2.33           0.20 
FC.HIGH.ENRICH   FC.NO.ENRICH 
         72.69         178.29 
FC.HIGH.ENRICH   FC.NO.ENRICH 
        19.215         31.400 
[1] "2.3 - 72.7 (19.2)"  "0.2 - 178.3 (31.4)"
[1] "hr=" "3.2"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
  FC.HIGH.ENRICH      10        1         4        0         5         0
  FC.NO.ENRICH       268       49       104        2        41         6
D2V3, multiclass
           clus
vv          FC.HIGH.ENRICH FC.NO.ENRICH
  STAGE I               10          268
  STAGE II               1           49
  STAGE III              4          104
  STAGE IV               0            2
  STAGE IVA              5           41
  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
  FC.HIGH.ENRICH   8   2   8   2
  FC.NO.ENRICH   133 160 156  21
D2V4, multiclass
    clus
vv   FC.HIGH.ENRICH FC.NO.ENRICH
  T1              8          133
  T2              2          160
  T3              8          156
  T4              2           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"
D2V5, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   7  11
  FC.NO.ENRICH   213 211
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    7   11
  FC.NO.ENRICH    213  211
   clus
vv  FC.HIGH.ENRICH FC.NO.ENRICH
  0              7          213
  1             11          211
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  13   0
  FC.NO.ENRICH   263   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   13    0
  FC.NO.ENRICH    263    9
   clus
vv  FC.HIGH.ENRICH FC.NO.ENRICH
  0             13          263
  1              0            9
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  14   6
  FC.NO.ENRICH   348 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   14    6
  FC.NO.ENRICH    348  124
        clus
vv       FC.HIGH.ENRICH FC.NO.ENRICH
  FEMALE             14          348
  MALE                6          124
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  11   8
  FC.NO.ENRICH   168 290
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   11    8
  FC.NO.ENRICH    168  290
     clus
vv    FC.HIGH.ENRICH FC.NO.ENRICH
  NO              11          168
  YES              8          290
[1] 2 2
[1] FALSE
                vv
clus             OTHER, SPECIFY THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL
  FC.HIGH.ENRICH              1                                            12
  FC.NO.ENRICH                6                                           336
                vv
clus             THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)
  FC.HIGH.ENRICH                                                                      2
  FC.NO.ENRICH                                                                      100
                vv
clus             THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
  FC.HIGH.ENRICH                                                                   5
  FC.NO.ENRICH                                                                    30
D2V9, multiclass
                                                                        clus
vv                                                                       FC.HIGH.ENRICH
  OTHER, SPECIFY                                                                      1
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                      12
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)              2
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)                 5
                                                                        clus
vv                                                                       FC.NO.ENRICH
  OTHER, SPECIFY                                                                    6
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL                                   336
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)          100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  14   2
  FC.NO.ENRICH   401  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   14    2
  FC.NO.ENRICH    401   15
     clus
vv    FC.HIGH.ENRICH FC.NO.ENRICH
  NO              14          401
  YES              2           15
[1] 2 2
[1] FALSE
                vv
clus             MINIMAL (T3) MODERATE/ADVANCED (T4A) NONE VERY ADVANCED (T4B)
  FC.HIGH.ENRICH            6                       3   10                   0
  FC.NO.ENRICH            124                      15  318                   1
D2V11, multiclass
                         clus
vv                        FC.HIGH.ENRICH FC.NO.ENRICH
  MINIMAL (T3)                         6          124
  MODERATE/ADVANCED (T4A)              3           15
  NONE                                10          318
  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
  FC.HIGH.ENRICH  12   4   0   2
  FC.NO.ENRICH   367  47   4  28
D2V12, multiclass
    clus
vv   FC.HIGH.ENRICH FC.NO.ENRICH
  R0             12          367
  R1              4           47
  R2              0            4
  RX              2           28
[1] 4 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
  FC.HIGH.ENRICH  11   7
  FC.NO.ENRICH   210 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   11    7
  FC.NO.ENRICH    210  255
            clus
vv           FC.HIGH.ENRICH FC.NO.ENRICH
  MULTIFOCAL             11          210
  UNIFOCAL                7          255
[1] 2 2
[1] FALSE
D2V15, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.ENRICH                                0     0
  FC.NO.ENRICH                                  1    51
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH                         3    14
  FC.NO.ENRICH                          23   308
D2V16, multiclass
                                  clus
vv                                 FC.HIGH.ENRICH FC.NO.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE              0            1
  ASIAN                                         0           51
  BLACK OR AFRICAN AMERICAN                     3           23
  WHITE                                        14          308
[1] 4 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
  FC.HIGH.ENRICH   1  16
  FC.NO.ENRICH    37 335
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    1   16
  FC.NO.ENRICH     37  335
                        clus
vv                       FC.HIGH.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  1           37
  NOT HISPANIC OR LATINO             16          335
[1] 2 2
[1] FALSE
