[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/19775034/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BLCA-TP/19921873/APOBEC_clinical_corr_input_19929340/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  136  213 
   0 HIGH  LOW 
  46  136  213 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          327            46            22 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          327            46            22 
[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=261,	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 
224  46  75   9 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
224  46  75   9 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
224  46  75   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
224  46  75   9 
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  84  52
  LOW  117  95
   0 HIGH  LOW 
  45  136  212 
   0 HIGH  LOW 
  27   52   95 
$`0`
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-C4-A0F7 TCGA-CF-A3MF TCGA-CF-A47S 
       34.98         6.58        17.56         2.04        12.59        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.66        12.10        13.12        18.58        13.08        12.92 
TCGA-CU-A0YR TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6T 
       15.12        13.58         8.15        53.29        76.60        18.81 
TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A6ME TCGA-FD-A3B4 TCGA-FD-A3N5 TCGA-FD-A43S 
        2.24        26.24        24.03        16.77        22.52        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TI TCGA-FJ-A871 
       20.91        26.73         2.70        13.35         9.67         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-UY-A78N TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAMH 
       64.01        21.24        86.83         5.98        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN8 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RM 
       54.90         8.32         3.88        35.84         3.48        47.84 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA5N 
       19.69         8.61         5.52 

$HIGH
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       24.13       104.65       108.95        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        50.04         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        12.79        12.56        12.62        18.48        29.79 
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 
       17.95       142.78         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        66.05        36.66        38.24       166.03        19.00 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E5-A4U1 
       13.64        13.64        56.15        11.18        15.35        38.83 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV 
       22.16        25.58         0.66         4.24         0.92         1.22 
TCGA-E7-A7XN TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43P 
       14.07        33.04        29.16         5.52        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-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
       12.36         3.06        31.07        61.94        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       59.31        33.01        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P 
       70.32         8.94         7.73         2.10         2.20        10.92 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A6ZA 
        4.73        10.65        32.98        19.10        19.82        22.72 
TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
       19.40        12.16        27.68        17.72        15.42        16.27 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V 
       50.56        35.97        44.38         1.15        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        16.54        38.99        17.62        37.05 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SM 
       29.56         3.85        51.32        79.66         3.22        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 
       14.93         4.21        21.04        26.27        66.64        13.74 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 
      110.60         7.63        44.32        56.48        61.45        75.39 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RG TCGA-ZF-A9RL 
       22.36        30.28        21.86        94.29        58.72        88.87 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
       59.38        63.02        56.35        57.90 

$LOW
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA82 
       11.97        94.88         8.35        44.94        16.83        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        47.80        29.65         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20O 
        7.33         2.66         6.74        12.39        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       17.88        19.50        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       17.16        20.48         9.96        28.70        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MG 
        8.98         1.94         2.93        23.01        13.97        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
       13.08        12.16        12.46        12.26        12.00        12.10 
TCGA-CF-A9FF TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA 
       11.87         4.90         5.19        13.58        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        46.68         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY 
       87.32         4.80        17.72         9.67        10.55       163.30 
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-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6X TCGA-DK-AA76 TCGA-DK-AA77 
       15.02        13.58       165.73        15.35        12.03        20.32 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 
       43.59        29.72         0.10        16.70         0.56        26.96 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       24.66        13.68        12.95        14.37         8.09        32.02 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94         4.01        12.62        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N 
       23.41        17.98        25.74        46.78        19.79         7.56 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TH 
       18.08        58.92         7.10        12.69         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
       10.85        12.66        10.65        17.23         3.25        11.08 
TCGA-G2-A2EC TCGA-G2-A2EK TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       22.88        15.95         7.23        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81        19.13        15.91        14.07        17.75        24.92 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R 
       13.91         3.12        20.98         7.36        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        32.78        20.05         5.62         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       21.34        20.28         8.48        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51        38.60         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO 
        2.76         9.14         9.07        11.70         1.81        11.80 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-LC-A66R TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G0 
       52.73        46.98        15.32        12.23        16.67        12.43 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        76.01        69.34         3.91        17.82         6.21 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        15.98        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        18.15 
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        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N 
       31.20        28.41        13.41        64.08        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       34.06        60.16        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        12.23 

   0 HIGH  LOW 
2.04 0.62 0.10 
     0   HIGH    LOW 
 92.98 166.03 165.73 
    0  HIGH   LOW 
13.58 19.25 16.06 
[1] "2.0 - 93.0 (13.6)"  "0.6 - 166.0 (19.2)" "0.1 - 165.7 (16.1)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IV
  0          1       16        17       12
  HIGH       0       46        46       44
  LOW        1       60        72       78
D1V3, multiclass
           clus
vv           0 HIGH LOW
  STAGE I    1    0   1
  STAGE II  16   46  60
  STAGE III 17   46  72
  STAGE IV  12   44  78
[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       37  66  20
  LOW        60 107  29
D1V4, multiclass
          clus
vv           0 HIGH LOW
  T0+T1+T2  19   37  60
  T3        17   66 107
  T4         8   20  29
[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  78  16  22   5
  LOW  115  25  48   4
D1V5, multiclass
    clus
vv     0 HIGH LOW
  N0  31   78 115
  N1   5   16  25
  N2   5   22  48
  N3   0    5   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 69  3
  LOW  97  7
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23    1
  HIGH   69    3
  LOW    97    7
   clus
vv   0 HIGH LOW
  0 23   69  97
  1  1    3   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  25 111
  LOW   64 149
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      13   33
  HIGH   25  111
  LOW    64  149
        clus
vv         0 HIGH LOW
  FEMALE  13   25  64
  MALE    33  111 149
[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 124   4
  LOW  191   9
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      35    6
  HIGH  124    4
  LOW   191    9
     clus
vv      0 HIGH LOW
  NO   35  124 191
  YES   6    4   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     8                         5   119
  LOW     18                        13   171
D1V12, multiclass
                           clus
vv                            0 HIGH LOW
  ASIAN                      13    8  18
  BLACK OR AFRICAN AMERICAN   4    5  13
  WHITE                      27  119 171
[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   2 119
  LOW    5 194
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       1   42
  HIGH    2  119
  LOW     5  194
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       1    2   5
  NOT HISPANIC OR LATINO  42  119 194
[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   190 136
  FC.LOW.NONSIG  18  27
  FC.NEUTRAL     11  11
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          326            45            22 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          136            27            11 
$FC.HIGH.SIG
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         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 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80        29.65         2.50        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        13.15        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        28.70        36.43        28.41         8.98 
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-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90        18.48         5.19        29.79         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       21.86         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78        87.32         4.80         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        23.21         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
      163.30        66.05        17.98        64.18        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       50.70        36.66        38.24        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       11.18        12.03        20.32        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72        22.16        16.70        25.58         0.56         0.66 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
        4.24        24.66         0.92         1.22        13.68        14.07 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37         8.09        32.02         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.62        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       27.35         3.62        53.88        11.01         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       27.45        58.92         7.10         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EC 
       10.85        31.07        17.23         3.25        11.08        22.88 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       61.94        48.00        15.95        26.93        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
        7.23        20.12        17.62        66.02         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       29.36        21.40        20.71        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       14.07        17.75        24.92         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98         7.00        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       19.82         8.48        36.49        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72         1.51        19.40        38.60         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       25.02         3.45         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       50.56        35.97        46.98        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.58        13.48        12.23        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.54        12.43        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        3.85        51.32         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
        4.21        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       10.82       110.60         7.63        71.57        91.73         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        98.99        44.32        56.48        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       27.06        75.39         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       22.36        25.41        21.11        31.20        30.28        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       28.41        94.29        13.41        64.08        58.72        88.87 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89        34.06        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        12.23 

$FC.LOW.NONSIG
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A42B TCGA-C4-A0F7 TCGA-CF-A3MF TCGA-CF-A47S 
       34.98         6.58        17.56         2.04        12.59        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A5U8 TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.66        12.10        13.12        18.58        13.08        12.92 
TCGA-CU-A0YR TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6T 
       15.12        13.58         8.15        53.29        76.60        18.81 
TCGA-E7-A4XJ TCGA-E7-A678 TCGA-E7-A6ME TCGA-FD-A3B4 TCGA-FD-A3N5 TCGA-FD-A43S 
        2.24        26.24        24.03        16.77        22.52        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TI TCGA-FJ-A871 
       20.91        26.73         2.70        13.35         9.67         8.94 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-UY-A78N TCGA-XF-A9SU TCGA-XF-AAME TCGA-XF-AAMH 
       64.01        21.24        86.83         5.98        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN8 TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RM 
       54.90         8.32         3.88        35.84         3.48        47.84 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA5N 
       19.69         8.61         5.52 

$FC.NEUTRAL
TCGA-5N-A9KM TCGA-BT-A20W TCGA-C4-A0F0 TCGA-CF-A3MH TCGA-CF-A5UA TCGA-DK-A1A7 
       17.42         8.35         1.94        13.08        12.00        18.41 
TCGA-DK-AA6M TCGA-E7-A3Y1 TCGA-E7-A677 TCGA-E7-A85H TCGA-FD-A3N6 TCGA-FD-A5BU 
       52.01         0.10        26.96        12.95        27.98        19.33 
TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-GV-A3JV TCGA-GV-A3QF 
        5.36        18.08        12.66        10.65        14.27        20.28 
TCGA-K4-A4AB TCGA-XF-A9SV TCGA-XF-AAN1 TCGA-XF-AAN7 
        2.76        12.76        30.94        18.15 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.56          2.04          0.10 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       166.03         92.98         52.01 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       17.670        13.580        13.675 
[1] "0.6 - 166.0 (17.7)" "2.0 - 93.0 (13.6)"  "0.1 - 52.0 (13.7)" 
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  FC.HIGH.SIG         1       97       113      115
  FC.LOW.NONSIG       1       16        17       12
  FC.NEUTRAL          0        9         5        7
D2V3, multiclass
           clus
vv          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I             1             1          0
  STAGE II           97            16          9
  STAGE III         113            17          5
  STAGE IV          115            12          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         89 166  45
  FC.LOW.NONSIG       19  17   8
  FC.NEUTRAL           8   7   4
D2V4, multiclass
          clus
vv         FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T0+T1+T2          89            19          8
  T3               166            17          7
  T4                45             8          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   178  39  66   8
  FC.LOW.NONSIG  31   5   5   0
  FC.NEUTRAL     15   2   4   1
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0         178            31         15
  N1          39             5          2
  N2          66             5          4
  N3           8             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   155   8
  FC.LOW.NONSIG  23   1
  FC.NEUTRAL     11   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    155    8
  FC.LOW.NONSIG   23    1
  FC.NEUTRAL      11    2
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0         155            23         11
  1           8             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    82 245
  FC.LOW.NONSIG  13  33
  FC.NEUTRAL      7  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     82  245
  FC.LOW.NONSIG   13   33
  FC.NEUTRAL       7   15
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          82            13          7
  MALE           245            33         15
[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.SIG   297  11
  FC.LOW.NONSIG  35   6
  FC.NEUTRAL     18   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    297   11
  FC.LOW.NONSIG   35    6
  FC.NEUTRAL      18    2
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO          297            35         18
  YES          11             6          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"
D2V9, continuous
D2V10, continuous
D2V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG      22                        16   276
  FC.LOW.NONSIG    13                         4    27
  FC.NEUTRAL        4                         2    14
D2V12, multiclass
                           clus
vv                          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ASIAN                              22            13          4
  BLACK OR AFRICAN AMERICAN          16             4          2
  WHITE                             276            27         14
[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.SIG     7 292
  FC.LOW.NONSIG   1  42
  FC.NEUTRAL      0  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      7  292
  FC.LOW.NONSIG    1   42
  FC.NEUTRAL       0   21
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               7             1          0
  NOT HISPANIC OR LATINO         292            42         21
[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"
