[1] "ofn"        "-oTBLCA-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/BLCA-TP/15076720/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BLCA-TP/15185889/APOBEC_clinical_corr_input_15190444/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=393, in cluster file=395, common to both=376
[1]   2 376
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  46  126  204 
   0 HIGH  LOW 
  46  126  204 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          315            46            15 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          315            46            15 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 376 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=136,	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=245,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	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=3,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'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 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=28,	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 376 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
 [9] "NUMBER_OF_LYMPH_NODES"       "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  2   3 109 179  52 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     114      179       52 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  2   3 109 179  52 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     114      179       52 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
213  41  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
213  41  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
213  41  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
213  41  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=69, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2    0   1
  0     21  22
  HIGH  85  41
  LOW  113  88
   0 HIGH  LOW 
  43  126  201 
   0 HIGH  LOW 
  22   41   88 
$`0`
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-C4-A0F7 TCGA-CF-A47S TCGA-CF-A47T 
       34.98         6.58        17.56         2.04        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A3IL 
       12.10        13.12        13.08        12.92         7.20        13.58 
TCGA-DK-A3IM TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6T TCGA-E7-A4XJ TCGA-E7-A678 
        7.82        41.56        76.60        12.36         2.24        13.97 
TCGA-E7-A6ME TCGA-FD-A3B4 TCGA-FD-A3N5 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR 
       12.99        16.77        22.52        14.96        20.91        26.73 
TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A871 
       19.33         2.70        13.35         9.67         7.13         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-UY-A78N TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
        3.06        21.24        86.83        92.98        11.31        54.90 
TCGA-XF-AAMW TCGA-XF-AAN8 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-AA4U 
        8.32         3.88        27.19         3.48        47.84         8.61 
TCGA-ZF-AA5N 
        5.52 

$HIGH
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       22.29       103.50       105.70        16.27        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       27.62        49.12         0.62        41.75        15.12        10.22 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A3PH 
       13.15        19.04         5.06        14.89        16.18         4.67 
TCGA-BT-A3PJ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A47X TCGA-CU-A3KJ TCGA-CU-A3YL 
       12.82         0.46         0.43        12.62         5.46        16.31 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC 
        1.84        21.86         2.14        66.41        16.70       130.88 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       10.59       123.85         8.22        50.27        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3X1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6U 
       20.81        48.00        30.67        38.24       166.03        10.49 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ 
        8.65        13.64        43.50        15.35        38.83         0.49 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B6 
       17.39         0.66         0.92         1.22        14.07        33.04 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BX 
       29.16         5.52        12.85        27.35         3.62         5.69 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.36         3.06 
TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE 
       31.07        61.94        30.61        26.93        35.24        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A6I1 TCGA-GD-A2C5 
       17.62        66.02         6.94        64.44         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        2.10         2.20        10.92         4.73        10.65        32.98 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A54R 
       19.10        19.82        22.72        19.40         8.22        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.74         1.81        15.42         6.38        15.58        13.48 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84         3.75        31.56        17.62        37.05 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SY TCGA-XF-A9T0 
       29.56         1.64        79.66         3.22        21.04        26.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMZ TCGA-XF-AAN0 
       66.64        13.74       110.60         7.63        44.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       61.45        75.39        18.64        30.28        21.86        74.56 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
       52.60        82.49        59.38        63.02        38.73        57.90 

$LOW
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA82 
       11.97        91.63         8.35        44.94        16.83        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        12.39        32.84        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD 
       14.96         5.06         8.35         8.25        17.16        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        28.70        24.26        28.41         8.98         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47Y TCGA-CF-A5UA 
        2.93        23.01         0.69        12.46        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A7 
       12.10        11.87         4.90         5.19        13.58        18.41 
TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3WX 
        7.79        87.32         2.20        17.72         9.67        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
      140.81        17.98        64.18        67.36        15.68        41.06 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.02        13.58         7.53        12.03        10.62        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MF 
       24.66         0.10        16.70         0.56        14.56        14.33 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
       13.68        12.95        14.37         8.09        32.02         8.94 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A5BS 
       17.98        25.74        46.78        19.79        22.98        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       11.01         5.36         8.25        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZE 
        7.10        12.69         2.27         4.31        10.85        10.65 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A2ES 
       17.23         3.25         6.48        22.88        15.95        33.01 
TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.23        19.46        21.40         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ 
       15.91        14.07        17.75        24.92        13.91         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
       20.98         7.36        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QF 
       20.05         5.62         7.00        14.27        21.34        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        8.48        10.59        27.35         8.58        19.07         1.51 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       38.60         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-AAQO TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
        9.07        11.70        11.80        15.32        12.23        16.67 
TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD 
       12.43        22.68        76.01        65.75        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
        4.54         1.87        17.88        48.62        64.80        66.41 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        23.64        28.24        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       16.27         2.10        10.82        71.57        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
        6.77        98.99        30.94        86.30        27.06        18.81 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        9.63         0.66        11.97        13.64         7.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N 
       24.13        28.41        13.41        52.73        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       34.06        19.69        60.16        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       47.15        19.17        10.13 

   0 HIGH  LOW 
2.04 0.43 0.10 
     0   HIGH    LOW 
 92.98 166.03 140.81 
    0  HIGH   LOW 
12.99 17.62 15.32 
[1] "2.0 - 93.0 (13.0)"  "0.4 - 166.0 (17.6)" "0.1 - 140.8 (15.3)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IV
  0          2       17        16       11
  HIGH       1       42        40       40
  LOW        1       58        66       77
D1V3, multiclass
           clus
vv           0 HIGH LOW
  STAGE I    2    1   1
  STAGE II  17   42  58
  STAGE III 16   40  66
  STAGE IV  11   40  77
[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   T0+T1+T2  T3  T4
  0          22  15   7
  HIGH       35  60  18
  LOW        57 104  27
D1V4, multiclass
          clus
vv           0 HIGH LOW
  T0+T1+T2  22   35  57
  T3        15   60 104
  T4         7   18  27
[1] 3 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    N0  N1  N2  N3
  0     33   4   4   0
  HIGH  72  14  22   4
  LOW  108  23  49   4
D1V5, multiclass
    clus
vv     0 HIGH LOW
  N0  33   72 108
  N1   4   14  23
  N2   4   22  49
  N3   0    4   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"
D1V6, binary
      cls
clus    0  1
  0    24  1
  HIGH 65  2
  LOW  93  7
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      24    1
  HIGH   65    2
  LOW    93    7
   clus
vv   0 HIGH LOW
  0 24   65  93
  1  1    2   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"
D1V7, binary
      cls
clus     0   1
  0     13  33
  HIGH  24 102
  LOW   59 145
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      13   33
  HIGH   24  102
  LOW    59  145
        clus
vv         0 HIGH LOW
  FEMALE  13   24  59
  MALE    33  102 145
[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, continuous
D1V9, continuous
D1V10, continuous
      vv
clus   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0       13                         5    26
  HIGH     8                         5   110
  LOW     17                        11   165
D1V11, multiclass
                           clus
vv                            0 HIGH LOW
  ASIAN                      13    8  17
  BLACK OR AFRICAN AMERICAN   5    5  11
  WHITE                      26  110 165
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
      cls
clus     0   1
  0      1  42
  HIGH   2 111
  LOW    5 185
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       1   42
  HIGH    2  111
  LOW     5  185
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       1    2   5
  NOT HISPANIC OR LATINO  42  111 185
[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.SIG   192 120
  FC.LOW.NONSIG  21  22
  FC.NEUTRAL      6   9
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          312            43            15 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          120            22             9 
$FC.HIGH.SIG
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       22.29        11.97        91.63       103.50       105.70         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       49.12         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        33.83        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
        6.74        12.39        13.15        19.04        32.84        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.25        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F1 
        9.96        28.70        24.26        28.41         8.98         2.93 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47V TCGA-CF-A47X 
       23.01         0.46         0.43         0.69        12.46        12.62 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3KJ 
       12.26        12.00        12.10        11.87         4.90         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        16.31         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        19.00        16.70       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         2.20         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       140.81        48.00 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        64.18        67.36        15.68        41.06        30.67 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       38.24        15.02        13.58       166.03        10.49         8.65 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
        7.53        13.64        43.50        12.03        10.62        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A541 
       15.35        38.83        24.66         0.49        16.70        17.39 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        0.56         0.66        14.33         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.07        14.37         8.09        32.02         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        22.98        27.35         3.62        53.88        11.01 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69         8.25        27.45        58.92         7.10         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       62.86        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE 
        3.06         4.31        10.85        31.07        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        6.48        22.88        61.94        30.61        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       35.24        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        64.44        19.46        21.40         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
        4.50        15.91        14.07        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        7.36        10.92        11.31        11.31         7.63        27.09 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        10.59 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       27.35         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC 
       38.60         9.01         8.22        25.02         3.45         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       27.68         9.07        11.70         1.74         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        6.38        11.80        15.32        15.58        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84         3.75        12.43        31.56 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        76.01        65.75        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A8HI 
       29.56        17.82         4.54         1.64         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SW 
       48.62        64.80        79.66         3.22        66.41        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64         2.10        13.74        10.82       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57        91.73         2.96         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       44.32        56.48        61.45        86.30        27.06        75.39 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        9.63         0.66        11.97        13.64        18.64         7.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       21.11        24.13        30.28        21.86        28.41        74.56 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N 
       13.41        52.73        52.60        82.49        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        59.38        60.16        63.02        38.73        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40         8.52        47.15        19.17        10.13 

$FC.LOW.NONSIG
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-C4-A0F7 TCGA-CF-A47S TCGA-CF-A47T 
       34.98         6.58        17.56         2.04        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A3IL 
       12.10        13.12        13.08        12.92         7.20        13.58 
TCGA-DK-A3IM TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6T TCGA-E7-A4XJ TCGA-E7-A678 
        7.82        41.56        76.60        12.36         2.24        13.97 
TCGA-E7-A6ME TCGA-FD-A3B4 TCGA-FD-A3N5 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BR 
       12.99        16.77        22.52        14.96        20.91        26.73 
TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A871 
       19.33         2.70        13.35         9.67         7.13         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-UY-A78N TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
        3.06        21.24        86.83        92.98        11.31        54.90 
TCGA-XF-AAMW TCGA-XF-AAN8 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-AA4U 
        8.32         3.88        27.19         3.48        47.84         8.61 
TCGA-ZF-AA5N 
        5.52 

$FC.NEUTRAL
TCGA-BT-A20W TCGA-C4-A0F0 TCGA-DK-A1A7 TCGA-E7-A3Y1 TCGA-E7-A677 TCGA-E7-A85H 
        8.35         1.94        18.41         0.10        14.56        12.95 
TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FJ-A3ZE TCGA-GV-A3JV TCGA-K4-A4AB TCGA-XF-A9SV 
        5.36        18.08        10.65        14.27         2.76        12.76 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-ZF-AA4T 
       30.94        18.81        19.69 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.43          2.04          0.10 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       166.03         92.98         30.94 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        16.49         12.99         12.95 
[1] "0.4 - 166.0 (16.5)" "2.0 - 93.0 (13.0)"  "0.1 - 30.9 (12.9)" 
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  FC.HIGH.SIG         2       96       102      110
  FC.LOW.NONSIG       2       17        16       11
  FC.NEUTRAL          0        4         4        7
D2V3, multiclass
           clus
vv          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I             2             2          0
  STAGE II           96            17          4
  STAGE III         102            16          4
  STAGE IV          110            11          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"
               vv
clus            T0+T1+T2  T3  T4
  FC.HIGH.SIG         89 158  41
  FC.LOW.NONSIG       22  15   7
  FC.NEUTRAL           3   6   4
D2V4, multiclass
          clus
vv         FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T0+T1+T2          89            22          3
  T3               158            15          6
  T4                41             7          4
[1] 3 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             N0  N1  N2  N3
  FC.HIGH.SIG   172  35  67   7
  FC.LOW.NONSIG  33   4   4   0
  FC.NEUTRAL      8   2   4   1
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0         172            33          8
  N1          35             4          2
  N2          67             4          4
  N3           7             0          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"
D2V6, binary
               cls
clus              0   1
  FC.HIGH.SIG   151   7
  FC.LOW.NONSIG  24   1
  FC.NEUTRAL      7   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    151    7
  FC.LOW.NONSIG   24    1
  FC.NEUTRAL       7    2
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0         151            24          7
  1           7             1          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"
D2V7, binary
               cls
clus              0   1
  FC.HIGH.SIG    80 235
  FC.LOW.NONSIG  13  33
  FC.NEUTRAL      3  12
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     80  235
  FC.LOW.NONSIG   13   33
  FC.NEUTRAL       3   12
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          80            13          3
  MALE           235            33         12
[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"
D2V8, continuous
D2V9, continuous
D2V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG      23                        16   264
  FC.LOW.NONSIG    13                         5    26
  FC.NEUTRAL        2                         0    11
D2V11, multiclass
                           clus
vv                          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ASIAN                              23            13          2
  BLACK OR AFRICAN AMERICAN          16             5          0
  WHITE                             264            26         11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
               cls
clus              0   1
  FC.HIGH.SIG     7 282
  FC.LOW.NONSIG   1  42
  FC.NEUTRAL      0  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      7  282
  FC.LOW.NONSIG    1   42
  FC.NEUTRAL       0   14
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               7             1          0
  NOT HISPANIC OR LATINO         282            42         14
[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"
