[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/22506467/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BLCA-TP/22506785/APOBEC_clinical_corr_input_22536864/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=412, in cluster file=395, common to both=395
[1]   2 395
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  46  172  177 
   0 HIGH  LOW 
  46  172  177 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           327             22             46 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           327             22             46 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 395 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=157,	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=206,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'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 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=69,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'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 395 columns, 1 survival variables, and 12 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"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "NUMBER_OF_LYMPH_NODES"      
[11] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  1   3 112 190  57 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     116      190       57 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   3 112 190  57 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     116      190       57 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
225  46  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
225  46  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
225  46  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
225  46  75   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, 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=20, 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     18  27
  HIGH 109  62
  LOW   90  86
   0 HIGH  LOW 
  45  171  176 
   0 HIGH  LOW 
  27   62   86 
$`0`
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A6AW TCGA-DK-A6B0 
        2.04        18.58        12.92        15.12        53.29        76.60 
TCGA-FD-A5BR TCGA-FD-A6TI TCGA-UY-A78N TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAN8 
       26.73         9.67        86.83        11.31        54.90         3.88 
TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-CF-A3MF 
        3.48        19.69        34.98         6.58        17.56        12.59 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FM TCGA-DK-A3IL 
       10.95        12.66        12.10        13.12        13.08        13.58 
TCGA-DK-A3IM TCGA-DK-AA6T TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A6ME TCGA-FD-A3B4 
        8.15        18.81         2.24        26.24        24.03        16.77 
TCGA-FD-A3N5 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62S TCGA-FJ-A871 
       22.52        14.96        20.91         2.70        13.35         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAMW TCGA-ZF-A9R5 
       64.01        21.24         5.98        92.98         8.32        35.84 
TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA5N 
       47.84         8.61         5.52 

$HIGH
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A3PJ 
      108.95        16.27        16.77        15.12        14.89        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC 
        9.96        28.70        18.48         2.14        16.70       130.88 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
        8.22        17.72        50.27        21.30        23.21        66.05 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       36.66        38.24       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       11.18        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        17.98        29.16        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        3.62         5.69         6.28        62.86        18.81         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY 
       12.36         3.06        31.07        17.23        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A6ZA 
       70.32        24.92        10.92        32.98        19.82        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X 
       25.02         3.45        27.68        50.56        35.97        14.24 
TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        1.84        51.32         3.22        34.45        14.93         4.21 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ 
       21.04        26.27        66.64        13.74         7.63        71.57 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
       44.32        61.45        86.30        30.28        94.29        88.87 
TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       57.90        24.13       104.65        17.16        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A0YX TCGA-BT-A20J 
        0.62        41.75        10.22        47.80        13.15        19.04 
TCGA-BT-A20R TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
        5.06        16.18         4.67        36.43        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CU-A3YL TCGA-CU-A5W6 
       12.79        12.56        13.97        12.62        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-AA6P 
       21.86        66.41        17.95       142.78        20.81        15.02 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KF TCGA-E7-A6MD 
       19.00        12.03        38.83        22.16         0.66         4.24 
TCGA-E7-A7XN TCGA-FD-A3SO TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       14.07         5.52        61.94        48.00        26.93        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       20.12        66.02         6.94        20.71        15.81        15.91 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A766 
        8.94        26.70         2.10         2.20        11.31        15.78 
TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A5NE 
        4.73        19.10         8.48        36.49        19.40        12.16 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-SY-A9G5 
       44.38         1.15        15.58        13.48        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9SG TCGA-XF-A9SI 
       17.62        37.05        29.56         3.85        48.62        79.66 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9R0 TCGA-ZF-A9R7 
      110.60         6.77        56.48        75.39        22.36        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
       28.41        58.72        59.38        60.16        67.20        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-GU-AATO 
       19.40        54.21        10.65 

$LOW
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-C4-A0EZ 
       33.83        12.39        26.14         8.35        20.48         8.98 
TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IV 
        4.90        13.58        19.00        46.68        87.32         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M 
       17.98        64.18        67.36        15.68        50.70        52.01 
TCGA-DK-AA6R TCGA-DK-AA77 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR 
      165.73        20.32         4.01        23.41        46.78        19.79 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TD 
       53.88        10.78         8.25        18.08        58.92        12.69 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A763 
        4.31        11.08        21.40        19.13        17.75        32.78 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AB 
       20.28        27.35         8.58        19.07         9.01         2.76 
TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-XF-A9SK TCGA-XF-A9SV 
        9.14        52.73        46.98        33.14        15.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMR 
       11.90        18.90         2.24         2.10        10.82        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       98.99        30.94        18.58         9.63        13.64        21.11 
TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       34.06        12.23        11.97        94.88         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       16.83        51.16        66.54         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         2.66         6.74        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-C4-A0F1 
       14.96         5.06         8.25        17.16         1.94         2.93 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A47Y TCGA-CF-A5UA 
       12.13        13.08        12.16        12.46        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
       12.10        11.87         5.19        18.41       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3WX TCGA-DK-A3WY 
       17.62        15.62         7.79         4.80        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 
       13.58        15.35        43.59        29.72         5.36        16.70 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.56        26.96        24.66        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SP 
        8.09        32.02         8.94        12.62        27.98        25.74 
TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF 
       22.98        19.33         5.36        27.45         7.10         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EK 
       10.85        12.66        10.65         3.25        22.88        15.95 
TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
        7.23        29.36        14.07        13.91         3.12        20.98 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97         7.63        20.05         7.00        14.27        21.34 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A5RI TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.51        38.60        11.70        15.32        12.23        16.67 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        76.01        69.34        35.24        17.82         6.21 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
        1.87        17.88        64.80        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       16.27         2.96        27.06         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA52 
       31.20        13.41        64.08        20.22         2.89        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        29.49 

   0 HIGH  LOW 
2.04 0.62 0.56 
     0   HIGH    LOW 
 92.98 166.03 165.73 
    0  HIGH   LOW 
13.58 19.82 16.06 
[1] "2.0 - 93.0 (13.6)"  "0.6 - 166.0 (19.8)" "0.6 - 165.7 (16.1)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IV
  0          1       16        17       12
  HIGH       0       58        63       51
  LOW        1       48        55       71
D1V3, multiclass
           clus
vv           0 HIGH LOW
  STAGE I    1    0   1
  STAGE II  16   58  48
  STAGE III 17   63  55
  STAGE IV  12   51  71
[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          19 17  8
  HIGH       46 85 23
  LOW        51 88 26
D1V4, multiclass
          clus
vv          0 HIGH LOW
  T0+T1+T2 19   46  51
  T3       17   85  88
  T4        8   23  26
[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     31   5   5   0
  HIGH 106  18  27   4
  LOW   88  23  43   4
D1V5, multiclass
    clus
vv     0 HIGH LOW
  N0  31  106  88
  N1   5   18  23
  N2   5   27  43
  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    23  1
  HIGH 82  4
  LOW  84  6
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23    1
  HIGH   82    4
  LOW    84    6
   clus
vv   0 HIGH LOW
  0 23   82  84
  1  1    4   6
[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  33 139
  LOW   56 121
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      13   33
  HIGH   33  139
  LOW    56  121
        clus
vv         0 HIGH LOW
  FEMALE  13   33  56
  MALE    33  139 121
[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     35   6
  HIGH 156   5
  LOW  159   9
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      35    6
  HIGH  156    5
  LOW   159    9
     clus
vv      0 HIGH LOW
  NO   35  156 159
  YES   6    5   9
[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"
D1V9, continuous
D1V10, continuous
D1V11, continuous
      vv
clus   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0       13                         4    27
  HIGH     9                         7   150
  LOW     17                        11   140
D1V12, multiclass
                           clus
vv                            0 HIGH LOW
  ASIAN                      13    9  17
  BLACK OR AFRICAN AMERICAN   4    7  11
  WHITE                      27  150 140
[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"
D1V13, binary
      cls
clus     0   1
  0      1  42
  HIGH   3 152
  LOW    4 161
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       1   42
  HIGH    3  152
  LOW     4  161
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       1    3   4
  NOT HISPANIC OR LATINO  42  152 161
[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 188 137
  FC.LOW.ENRICH   11  11
  FC.NO.ENRICH    18  27
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           325             22             45 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           137             11             27 
$FC.HIGH.ENRICH
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14        14.89        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        8.98         4.90        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70       130.88        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS 
       46.78        19.79        12.85        27.35         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       10.78         5.69         8.25        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
       31.07        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        19.82        27.35         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
        9.01        25.02         3.45         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       50.56        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        13.74        10.82         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-YC-A8S6 TCGA-YF-AA3M 
       98.99        44.32        61.45        86.30         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 
       21.11        30.28        94.29        88.87        34.06        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.74        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16        16.18         4.67        36.43        28.41 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG 
        2.93        23.01        12.79        12.56        13.97        12.13 
TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.16        12.46        12.62        12.26        12.10        11.87 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD 
        5.19        29.79         1.84        21.86        66.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q 
        4.80        20.81        10.55       163.30        15.02        13.58 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       19.00        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6MF 
       22.16        16.70         0.56         0.66         4.24        24.66 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
       13.68        14.07        14.37         8.09        32.02         8.94 
TCGA-FD-A3B8 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BZ TCGA-FD-A62O 
       12.62         5.52        25.74        22.98        27.45         7.10 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        2.27        10.85         3.25        22.88        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI 
        1.51        19.40        38.60        12.16         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34        35.24        29.56        17.82         6.21         3.85 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       23.64        28.24        16.27       110.60         2.96         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        75.39         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       25.41        31.20        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       58.72        20.22         2.89        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-GU-AATO 
       10.65 

$FC.LOW.ENRICH
TCGA-BT-A20W TCGA-DK-AA6M TCGA-FD-A5C0 TCGA-GV-A3QF TCGA-K4-A4AB TCGA-XF-A9SV 
        8.35        52.01        18.08        20.28         2.76        12.76 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-5N-A9KM TCGA-C4-A0F0 TCGA-CF-A3MH TCGA-CF-A5UA 
       30.94        18.58        17.42         1.94        13.08        12.00 
TCGA-DK-A1A7 TCGA-E7-A3Y1 TCGA-E7-A677 TCGA-E7-A85H TCGA-FD-A3N6 TCGA-FD-A5BU 
       18.41         5.36        26.96        12.95        27.98        19.33 
TCGA-FD-A5BV TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-GV-A3JV 
        5.36        12.66        10.65        14.27 

$FC.NO.ENRICH
TCGA-C4-A0F7 TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A6AW TCGA-DK-A6B0 
        2.04        18.58        12.92        15.12        53.29        76.60 
TCGA-FD-A5BR TCGA-FD-A6TI TCGA-UY-A78N TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAN8 
       26.73         9.67        86.83        11.31        54.90         3.88 
TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-CF-A3MF 
        3.48        19.69        34.98         6.58        17.56        12.59 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FM TCGA-DK-A3IL 
       10.95        12.66        12.10        13.12        13.08        13.58 
TCGA-DK-A3IM TCGA-DK-AA6T TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A6ME TCGA-FD-A3B4 
        8.15        18.81         2.24        26.24        24.03        16.77 
TCGA-FD-A3N5 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62S TCGA-FJ-A871 
       22.52        14.96        20.91         2.70        13.35         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAMW TCGA-ZF-A9R5 
       64.01        21.24         5.98        92.98         8.32        35.84 
TCGA-ZF-A9RM TCGA-ZF-AA4U TCGA-ZF-AA5N 
       47.84         8.61         5.52 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.56           1.94           2.04 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        166.03          52.01          92.98 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        17.880         13.675         13.580 
[1] "0.6 - 166.0 (17.9)" "1.9 - 52.0 (13.7)"  "2.0 - 93.0 (13.6)" 
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FC.HIGH.ENRICH       1       97       113      115
  FC.LOW.ENRICH        0        9         5        7
  FC.NO.ENRICH         1       16        17       12
D2V3, multiclass
           clus
vv          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                1             0            1
  STAGE II              97             9           16
  STAGE III            113             5           17
  STAGE IV             115             7           12
[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.ENRICH       89 166  45
  FC.LOW.ENRICH         8   7   4
  FC.NO.ENRICH         19  17   8
D2V4, multiclass
          clus
vv         FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T0+T1+T2             89             8           19
  T3                  166             7           17
  T4                   45             4            8
[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.ENRICH 179  39  66   7
  FC.LOW.ENRICH   15   2   4   1
  FC.NO.ENRICH    31   5   5   0
D2V5, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0            179            15           31
  N1             39             2            5
  N2             66             4            5
  N3              7             1            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"
D2V6, binary
                cls
clus               0   1
  FC.HIGH.ENRICH 155   8
  FC.LOW.ENRICH   11   2
  FC.NO.ENRICH    23   1
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  155    8
  FC.LOW.ENRICH    11    2
  FC.NO.ENRICH     23    1
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0            155            11           23
  1              8             2            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"
D2V7, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  82 245
  FC.LOW.ENRICH    7  15
  FC.NO.ENRICH    13  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   82  245
  FC.LOW.ENRICH     7   15
  FC.NO.ENRICH     13   33
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE             82             7           13
  MALE              245            15           33
[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, binary
                cls
clus               0   1
  FC.HIGH.ENRICH 297  11
  FC.LOW.ENRICH   18   3
  FC.NO.ENRICH    35   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  297   11
  FC.LOW.ENRICH    18    3
  FC.NO.ENRICH     35    6
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO             297            18           35
  YES             11             3            6
[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"
D2V9, continuous
D2V10, continuous
D2V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH    22                        16   276
  FC.LOW.ENRICH      4                         2    14
  FC.NO.ENRICH      13                         4    27
D2V12, multiclass
                           clus
vv                          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ASIAN                                 22             4           13
  BLACK OR AFRICAN AMERICAN             16             2            4
  WHITE                                276            14           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"
D2V13, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   7 292
  FC.LOW.ENRICH    0  21
  FC.NO.ENRICH     1  42
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    7  292
  FC.LOW.ENRICH     0   21
  FC.NO.ENRICH      1   42
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  7             0            1
  NOT HISPANIC OR LATINO            292            21           42
[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"
