[1] "ofn"        "-oTESCA-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/ESCA-TP/22506419/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/ESCA-TP/22533622/APOBEC_clinical_corr_input_22539540/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=185, in cluster file=185, common to both=185
[1]   2 185
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 145   20   20 
   0 HIGH  LOW 
 145   20   20 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            30             10            145 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            30             10            145 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 185 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=75,	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=96,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	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=4,	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:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=14,	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 185 columns, 1 survival variables, and 14 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] "HISTOLOGICAL_TYPE"           "NUMBER_PACK_YEARS_SMOKED"   
[11] "RESIDUAL_TUMOR"              "NUMBER_OF_LYMPH_NODES"      
[13] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, 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 31 43 88  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   32    43    88     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 31 43 88  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   32    43    88     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
77 69 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
77 69 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
77 69 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
77 69 12  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
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=46, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=14, 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    83 62
  HIGH 13  7
  LOW  12  8
   0 HIGH  LOW 
 145   20   20 
   0 HIGH  LOW 
  62    7    8 
$`0`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 
       20.12         3.88         9.30         0.53        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        9.96        14.86        14.50       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V 
        5.92        12.43        13.41        12.33        13.38        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39        12.85        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB 
       15.91        18.21        25.08        41.23        14.37         1.32 
TCGA-ZR-A9CJ 
       19.73 

$HIGH
TCGA-Q9-A6FU TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A8NK 
        5.16         0.85        18.64         0.79        68.02        13.55 
TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A4A8 TCGA-LN-A4A9 
       21.37        12.66        13.15        15.35        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A9FP TCGA-S8-A6BW TCGA-VR-A8EX TCGA-VR-AA7B TCGA-Z6-A8JD 
       13.22        12.03        20.38        28.11        11.24         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN 
        2.10         2.66 

$LOW
TCGA-IG-A3YB TCGA-IG-A51D TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-L5-A43H 
        2.63        17.03         4.67        12.16        44.75         0.30 
TCGA-L5-A88W TCGA-L5-A8NS TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HX 
       25.12        13.41        10.45        12.46        12.00        12.23 
TCGA-LN-A9FO TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EP 
        0.13         7.04        53.95        16.44         8.98        27.09 
TCGA-VR-A8EW TCGA-VR-AA7D 
        8.12         9.17 

   0 HIGH  LOW 
0.36 0.79 0.13 
     0   HIGH    LOW 
122.10  68.02  53.95 
     0   HIGH    LOW 
13.250 12.905 12.080 
[1] "0.4 - 122.1 (13.2)" "0.8 - 68.0 (12.9)"  "0.1 - 54.0 (12.1)" 
D1V2, continuous
      vv
clus   STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  0          8        5        3        1        29        26        25
  HIGH       0        0        2        0        11         2         0
  LOW        0        0        1        0         7         3         1
      vv
clus   STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  0            11          5          6        4         3
  HIGH          2          1          0        1         1
  LOW           1          3          1        0         0
D1V3, multiclass
            clus
vv            0 HIGH LOW
  STAGE I     8    0   0
  STAGE IA    5    0   0
  STAGE IB    3    2   1
  STAGE II    1    0   0
  STAGE IIA  29   11   7
  STAGE IIB  26    2   3
  STAGE III  25    0   1
  STAGE IIIA 11    2   1
  STAGE IIIB  5    1   3
  STAGE IIIC  6    0   1
  STAGE IV    4    1   0
  STAGE IVA   3    1   0
[1] 12  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       29 29 69  4
  HIGH     1  8 10  1
  LOW      2  6  9  0
D1V4, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 29    1   2
  T2    29    8   6
  T3    69   10   9
  T4     4    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"
      vv
clus   N0 N1 N2 N3
  0    53 62  8  6
  HIGH 15  3  1  1
  LOW   9  4  3  1
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 53   15   9
  N1 62    3   4
  N2  8    1   3
  N3  6    1   1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus     0   1
  0    103   7
  HIGH  17   2
  LOW   16   0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     103    7
  HIGH   17    2
  LOW    16    0
   clus
vv    0 HIGH LOW
  0 103   17  16
  1   7    2   0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
      cls
clus     0   1
  0     22 123
  HIGH   5  15
  LOW    0  20
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      22  123
  HIGH    5   15
  LOW     0   20
        clus
vv         0 HIGH LOW
  FEMALE  22    5   0
  MALE   123   15  20
[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    100  30
  HIGH  14   5
  LOW   10   8
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     100   30
  HIGH   14    5
  LOW    10    8
     clus
vv      0 HIGH LOW
  NO  100   14  10
  YES  30    5   8
[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, binary
      cls
clus    0  1
  0    84 61
  HIGH  0 20
  LOW   5 15
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      84   61
  HIGH    0   20
  LOW     5   15
                                   clus
vv                                   0 HIGH LOW
  ESOPHAGUS ADENOCARCINOMA, NOS     84    0   5
  ESOPHAGUS SQUAMOUS CELL CARCINOMA 61   20  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"
D1V11, continuous
      vv
clus    R0  R1  R2  RX
  0    106  10   2   4
  HIGH  17   1   0   2
  LOW   14   2   0   1
D1V12, multiclass
    clus
vv     0 HIGH LOW
  R0 106   17  14
  R1  10    1   2
  R2   2    0   0
  RX   4    2   1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
      vv
clus   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0       30                         5    92
  HIGH     8                         0    11
  LOW      8                         0    11
D1V14, multiclass
                           clus
vv                           0 HIGH LOW
  ASIAN                     30    8   8
  BLACK OR AFRICAN AMERICAN  5    0   0
  WHITE                     92   11  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"
D1V15, binary
      cls
clus    0  1
  0     6 60
  HIGH  0 15
  LOW   0 13
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       6   60
  HIGH    0   15
  LOW     0   13
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      6    0   0
  NOT HISPANIC OR LATINO 60   15  13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2             0  1
  FC.HIGH.ENRICH 19 11
  FC.LOW.ENRICH   6  4
  FC.NO.ENRICH   83 62
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            30             10            145 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            11              4             62 
$FC.HIGH.ENRICH
TCGA-Q9-A6FU TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 
        5.16         0.85         2.63        18.64        17.03         0.79 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49L 
       12.16        44.75        68.02        13.55        21.37        10.45 
TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.66        13.15        15.35        15.52        11.54        13.22 
TCGA-LN-A7HW TCGA-LN-A9FO TCGA-LN-A9FP TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8EW 
       12.00         0.13        12.03        20.38        27.09         8.12 
TCGA-VR-A8EX TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       28.11        11.24         9.17         3.42         2.10         2.66 

$FC.LOW.ENRICH
TCGA-IG-A8O2 TCGA-L5-A43H TCGA-L5-A88W TCGA-L5-A8NS TCGA-LN-A49Y TCGA-LN-A7HX 
        4.67         0.30        25.12        13.41        12.46        12.23 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-V5-A7RE TCGA-V5-AASX 
        7.04        53.95        16.44         8.98 

$FC.NO.ENRICH
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       27.12        20.02        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 
       20.12         3.88         9.30         0.53        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        9.96        14.86        14.50       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49V 
        5.92        12.43        13.41        12.33        13.38        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39        12.85        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       10.52        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB 
       15.91        18.21        25.08        41.23        14.37         1.32 
TCGA-ZR-A9CJ 
       19.73 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.13           0.30           0.36 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         68.02          53.95         122.10 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        12.095         12.345         13.250 
[1] "0.1 - 68.0 (12.1)"  "0.3 - 54.0 (12.3)"  "0.4 - 122.1 (13.2)"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FC.HIGH.ENRICH       0        0        2        0        15         4
  FC.LOW.ENRICH        0        0        1        0         3         1
  FC.NO.ENRICH         8        5        3        1        29        26
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FC.HIGH.ENRICH         0          3          3          1        1         1
  FC.LOW.ENRICH          1          0          1          0        0         0
  FC.NO.ENRICH          25         11          5          6        4         3
D2V3, multiclass
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                 0             0            8
  STAGE IA                0             0            5
  STAGE IB                2             1            3
  STAGE II                0             0            1
  STAGE IIA              15             3           29
  STAGE IIB               4             1           26
  STAGE III               0             1           25
  STAGE IIIA              3             0           11
  STAGE IIIB              3             1            5
  STAGE IIIC              1             0            6
  STAGE IV                1             0            4
  STAGE IVA               1             0            3
[1] 12  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     2 13 14  1
  FC.LOW.ENRICH      1  1  5  0
  FC.NO.ENRICH      29 29 69  4
D2V4, multiclass
       clus
vv      FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T0+T1              2             1           29
  T2                13             1           29
  T3                14             5           69
  T4                 1             0            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"
                vv
clus             N0 N1 N2 N3
  FC.HIGH.ENRICH 19  6  3  2
  FC.LOW.ENRICH   5  1  1  0
  FC.NO.ENRICH   53 62  8  6
D2V5, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0             19             5           53
  N1              6             1           62
  N2              3             1            8
  N3              2             0            6
[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  27   2
  FC.LOW.ENRICH    6   0
  FC.NO.ENRICH   103   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   27    2
  FC.LOW.ENRICH     6    0
  FC.NO.ENRICH    103    7
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0             27             6          103
  1              2             0            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"
D2V7, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   5  25
  FC.LOW.ENRICH    0  10
  FC.NO.ENRICH    22 123
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    5   25
  FC.LOW.ENRICH     0   10
  FC.NO.ENRICH     22  123
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE              5             0           22
  MALE               25            10          123
[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  20   9
  FC.LOW.ENRICH    4   4
  FC.NO.ENRICH   100  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   20    9
  FC.LOW.ENRICH     4    4
  FC.NO.ENRICH    100   30
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO              20             4          100
  YES              9             4           30
[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, binary
                cls
clus              0  1
  FC.HIGH.ENRICH  0 30
  FC.LOW.ENRICH   5  5
  FC.NO.ENRICH   84 61
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    0   30
  FC.LOW.ENRICH     5    5
  FC.NO.ENRICH     84   61
                                   clus
vv                                  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ESOPHAGUS ADENOCARCINOMA, NOS                  0             5           84
  ESOPHAGUS SQUAMOUS CELL CARCINOMA             30             5           61
[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"
D2V11, continuous
                vv
clus              R0  R1  R2  RX
  FC.HIGH.ENRICH  26   1   0   3
  FC.LOW.ENRICH    5   2   0   0
  FC.NO.ENRICH   106  10   2   4
D2V12, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  R0             26             5          106
  R1              1             2           10
  R2              0             0            2
  RX              3             0            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"
D2V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH    13                         0    15
  FC.LOW.ENRICH      3                         0     7
  FC.NO.ENRICH      30                         5    92
D2V14, multiclass
                           clus
vv                          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ASIAN                                 13             3           30
  BLACK OR AFRICAN AMERICAN              0             0            5
  WHITE                                 15             7           92
[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"
D2V15, binary
                cls
clus              0  1
  FC.HIGH.ENRICH  0 21
  FC.LOW.ENRICH   0  7
  FC.NO.ENRICH    6 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    0   21
  FC.LOW.ENRICH     0    7
  FC.NO.ENRICH      6   60
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  0             0            6
  NOT HISPANIC OR LATINO             21             7           60
[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"
