[1] "ofn"        "-oTLUSC-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/LUSC-TP/15084586/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/LUSC-TP/15165081/APOBEC_clinical_corr_input_15169729/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=495, in cluster file=177, common to both=177
[1]   2 177
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  67   43   67 
   0 HIGH  LOW 
  67   43   67 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           58            66            53 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           58            66            53 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 177 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=82,	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=140,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 177 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=37, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 36 115  14  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 36 115  14  12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 36 115  14  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 36 115  14  12 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
115  39  17   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
115  39  17   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
115  39  17   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
115  39  17   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=56, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=40, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
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    36 27
  HIGH 19 23
  LOW  32 32
   0 HIGH  LOW 
  63   42   64 
   0 HIGH  LOW 
  27   23   32 
$`0`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-4721 TCGA-18-5592 
        7.46        75.75       117.57        11.34       154.32        49.94 
TCGA-21-1070 TCGA-21-1081 TCGA-21-5786 TCGA-22-1002 TCGA-22-4591 TCGA-22-4599 
      119.54         9.34        33.93         4.31        20.48        38.17 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5492 
       13.12        11.77         0.79        71.34        30.12        16.64 
TCGA-33-4582 TCGA-33-4586 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 
      103.53        14.07        67.79        56.38        23.24        16.93 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 
        7.82         6.81         0.39         3.39        74.07        60.79 
TCGA-39-5039 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 
       17.88        22.49        27.02        18.38        24.89         5.46 
TCGA-51-4080 TCGA-51-4081 TCGA-56-1622 TCGA-56-6546 TCGA-60-2709 TCGA-60-2710 
        0.39        29.95        28.96         0.62        49.48        66.54 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       41.42        35.34        42.64        35.90        23.57        26.83 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 
       43.10        21.07         0.92         0.99        43.99         2.01 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
       23.01         2.01        40.01        30.02        10.06         4.01 
TCGA-66-2800 TCGA-85-6175 TCGA-85-6560 
       49.05         9.67        11.97 

$HIGH
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
       12.20        79.46         4.80        23.54        92.15         1.64 
TCGA-18-5595 TCGA-21-5782 TCGA-22-1011 TCGA-22-5473 TCGA-22-5477 TCGA-22-5491 
       27.19        31.63         1.74        63.55        44.25        56.32 
TCGA-33-4547 TCGA-33-4566 TCGA-33-6737 TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 
       79.53       174.08        19.76         2.63        61.61        65.23 
TCGA-34-5928 TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-39-5022 TCGA-39-5024 
       18.15         4.96         3.95         0.43        55.20        70.03 
TCGA-39-5028 TCGA-39-5031 TCGA-43-3920 TCGA-51-4079 TCGA-56-6545 TCGA-60-2698 
        1.71        27.39        33.11         0.39         2.04        10.22 
TCGA-60-2720 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 
        3.19        21.01        25.05         1.02         2.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 
        3.02        19.00        12.00         1.97        25.97         5.03 

$LOW
TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-21-1071 
       31.99        36.07        86.96         6.18         2.79        46.88 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 
       60.89        34.78        15.58        41.69        10.82         7.33 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4607 
       14.10        27.02        35.08        24.13        34.75        19.30 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5482 TCGA-22-5489 TCGA-33-4532 
       31.73        64.93        14.63        11.74        62.86         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-34-2608 TCGA-34-5236 TCGA-34-5240 
      133.74        98.01       151.27        32.88         9.07        12.00 
TCGA-34-5927 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 
       30.94        44.75        68.58        24.33         1.94        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-43-6143 TCGA-43-6770 TCGA-46-3768 TCGA-46-6025 
       35.64        35.70        12.36        21.47         9.99        10.65 
TCGA-46-6026 TCGA-56-5897 TCGA-56-5898 TCGA-60-2707 TCGA-60-2708 TCGA-60-2712 
       13.91         0.10        18.25        21.93        80.45         9.01 
TCGA-60-2713 TCGA-60-2721 TCGA-60-2722 TCGA-60-2726 TCGA-66-2727 TCGA-66-2744 
       56.91        32.32        29.85        11.77        16.96         0.99 
TCGA-66-2754 TCGA-66-2763 TCGA-66-2767 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
        2.01         0.99         2.01        12.03         3.98        24.95 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2794 TCGA-85-6561 
       22.98         4.04        54.08        12.99 

   0 HIGH  LOW 
0.39 0.39 0.10 
     0   HIGH    LOW 
154.32 174.08 151.27 
    0  HIGH   LOW 
23.24 19.00 21.70 
[1] "0.4 - 154.3 (23.2)" "0.4 - 174.1 (19.0)" "0.1 - 151.3 (21.7)"
D1V2, continuous
      vv
clus   STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  0          13       22        10         6          7          8        1
  HIGH        7       17         0         8          7          2        1
  LOW         7       31         3        12          9          4        1
D1V3, multiclass
            clus
vv            0 HIGH LOW
  STAGE IA   13    7   7
  STAGE IB   22   17  31
  STAGE IIA  10    0   3
  STAGE IIB   6    8  12
  STAGE IIIA  7    7   9
  STAGE IIIB  8    2   4
  STAGE IV    1    1   1
[1] 7 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   T1 T2 T3 T4
  0    18 36  6  7
  HIGH  8 28  4  3
  LOW  10 51  4  2
D1V4, multiclass
    clus
vv    0 HIGH LOW
  T1 18    8  10
  T2 36   28  51
  T3  6    4   4
  T4  7    3   2
[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    47 15  5  0
  HIGH 28  8  5  2
  LOW  40 16  7  3
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 47   28  40
  N1 15    8  16
  N2  5    5   7
  N3  0    2   3
[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    61  1
  HIGH 40  1
  LOW  63  1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      61    1
  HIGH   40    1
  LOW    63    1
   clus
vv   0 HIGH LOW
  0 61   40  63
  1  1    1   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"
D1V7, binary
      cls
clus    0  1
  0    20 47
  HIGH 11 32
  LOW  15 52
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      20   47
  HIGH   11   32
  LOW    15   52
        clus
vv        0 HIGH LOW
  FEMALE 20   11  15
  MALE   47   32  52
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
      vv
clus   LUNG BASALOID SQUAMOUS CELL CARCINOMA
  0                                        2
  HIGH                                     1
  LOW                                      2
      vv
clus   LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  0                                         1
  HIGH                                      0
  LOW                                       0
      vv
clus   LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  0                                                             64
  HIGH                                                          42
  LOW                                                           65
D1V9, multiclass
                                                             clus
vv                                                             0 HIGH LOW
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                        2    1   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                       1    0   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 64   42  65
[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"
D1V10, binary
      cls
clus    0  1
  0     0 67
  HIGH  0 43
  LOW   5 62
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       0   67
  HIGH    0   43
  LOW     5   62
     clus
vv     0 HIGH LOW
  NO   0    0   5
  YES 67   43  62
[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
D1V12, continuous
      vv
clus   R0 R1 R2 RX
  0    56  0  0  4
  HIGH 35  2  1  1
  LOW  55  0  3  5
D1V13, multiclass
    clus
vv    0 HIGH LOW
  R0 56   35  55
  R1  0    2   0
  R2  0    1   3
  RX  4    1   5
[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   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0        2                         5    41
  HIGH     1                         1    24
  LOW      2                         3    45
D1V14, multiclass
                           clus
vv                           0 HIGH LOW
  ASIAN                      2    1   2
  BLACK OR AFRICAN AMERICAN  5    1   3
  WHITE                     41   24  45
[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     0 40
  HIGH  0 21
  LOW   3 38
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       0   40
  HIGH    0   21
  LOW     3   38
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      0    0   3
  NOT HISPANIC OR LATINO 40   21  38
[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   28 28
  FC.LOW.NONSIG 36 26
  FC.NEUTRAL    23 28
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           56            62            51 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           28            26            28 
$FC.HIGH.SIG
TCGA-18-3406 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-5595 
       12.20         4.80        23.54        92.15         1.64        27.19 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-5782 TCGA-22-1011 
       46.88        60.89        34.78        15.58        31.63         1.74 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5491 TCGA-33-4533 
       19.30        63.55        14.63        44.25        56.32       133.74 
TCGA-33-4547 TCGA-33-6737 TCGA-34-2596 TCGA-34-2600 TCGA-34-5928 TCGA-34-5929 
       79.53        19.76         2.63        61.61        18.15         4.96 
TCGA-37-3783 TCGA-37-3789 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        3.95         0.43        55.20        70.03         1.71        24.33 
TCGA-39-5031 TCGA-39-5035 TCGA-43-3920 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       27.39        15.58        33.11        10.65        13.91         0.39 
TCGA-56-5897 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2720 TCGA-60-2721 
        0.10         2.04        10.22        21.93         3.19        32.32 
TCGA-60-2726 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 
       11.77        21.01        25.05         1.02         2.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
        3.02        19.00        12.00         1.97        25.97        22.98 
TCGA-66-2791 TCGA-66-2794 
        5.03        54.08 

$FC.LOW.NONSIG
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-4721 TCGA-18-5592 
        7.46        75.75       117.57        11.34       154.32        49.94 
TCGA-21-1070 TCGA-21-1081 TCGA-21-5786 TCGA-22-1002 TCGA-22-4591 TCGA-22-4599 
      119.54         9.34        33.93         4.31        20.48        38.17 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5492 
       13.12        11.77         0.79        71.34        30.12        16.64 
TCGA-33-4582 TCGA-33-4586 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-37-4133 
      103.53        14.07        67.79        56.38        23.24         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-39-5039 
        6.81         0.39         3.39        74.07        60.79        17.88 
TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-51-4080 
       22.49        27.02        18.38        24.89         5.46         0.39 
TCGA-51-4081 TCGA-56-1622 TCGA-56-6546 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       29.95        28.96         0.62        49.48        66.54        41.42 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-66-2734 
       35.34        42.64        35.90        23.57        26.83        43.10 
TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 TCGA-66-2770 
       21.07         0.92         0.99        43.99         2.01        23.01 
TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
        2.01        40.01        30.02        10.06         4.01        49.05 
TCGA-85-6175 TCGA-85-6560 
        9.67        11.97 

$FC.NEUTRAL
TCGA-18-3409 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       79.46        31.99        36.07        86.96         6.18         2.79 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 
       41.69        10.82         7.33        14.10        27.02        35.08 
TCGA-22-4595 TCGA-22-4601 TCGA-22-5471 TCGA-22-5472 TCGA-22-5482 TCGA-22-5489 
       24.13        34.75        31.73        64.93        11.74        62.86 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-34-2608 TCGA-34-5231 
        7.63        98.01       174.08       151.27        32.88        65.23 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-39-5019 TCGA-39-5021 
        9.07        12.00        16.93        30.94        44.75        68.58 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-6143 TCGA-43-6770 TCGA-46-3768 
        1.94        35.64        35.70        12.36        21.47         9.99 
TCGA-56-5898 TCGA-60-2708 TCGA-60-2712 TCGA-60-2713 TCGA-60-2722 TCGA-66-2727 
       18.25        80.45         9.01        56.91        29.85        16.96 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2763 TCGA-66-2767 TCGA-66-2780 TCGA-66-2781 
        0.99         2.01         0.99         2.01        12.03         3.98 
TCGA-66-2783 TCGA-66-2789 TCGA-85-6561 
       24.95         4.04        12.99 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.10          0.39          0.99 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       133.74        154.32        174.08 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       19.000        23.405        24.130 
[1] "0.1 - 133.7 (19.0)" "0.4 - 154.3 (23.4)" "1.0 - 174.1 (24.1)"
D2V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  FC.HIGH.SIG          9       25         1        11          8          3
  FC.LOW.NONSIG       13       21        10         6          7          8
  FC.NEUTRAL           5       24         2         9          8          3
               vv
clus            STAGE IV
  FC.HIGH.SIG          1
  FC.LOW.NONSIG        1
  FC.NEUTRAL           1
D2V3, multiclass
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE IA             9            13          5
  STAGE IB            25            21         24
  STAGE IIA            1            10          2
  STAGE IIB           11             6          9
  STAGE IIIA           8             7          8
  STAGE IIIB           3             8          3
  STAGE IV             1             1          1
[1] 7 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  FC.HIGH.SIG   10 40  4  4
  FC.LOW.NONSIG 18 35  6  7
  FC.NEUTRAL     8 40  4  1
D2V4, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1          10            18          8
  T2          40            35         40
  T3           4             6          4
  T4           4             7          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"
               vv
clus            N0 N1 N2 N3
  FC.HIGH.SIG   37 12  7  2
  FC.LOW.NONSIG 46 15  5  0
  FC.NEUTRAL    32 12  5  3
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0          37            46         32
  N1          12            15         12
  N2           7             5          5
  N3           2             0          3
[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   54  1
  FC.LOW.NONSIG 60  1
  FC.NEUTRAL    50  1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     54    1
  FC.LOW.NONSIG   60    1
  FC.NEUTRAL      50    1
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0          54            60         50
  1           1             1          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.SIG   15 43
  FC.LOW.NONSIG 20 46
  FC.NEUTRAL    11 42
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     15   43
  FC.LOW.NONSIG   20   46
  FC.NEUTRAL      11   42
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          15            20         11
  MALE            43            46         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"
D2V8, continuous
               vv
clus            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  FC.HIGH.SIG                                       0
  FC.LOW.NONSIG                                     2
  FC.NEUTRAL                                        3
               vv
clus            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  FC.HIGH.SIG                                        0
  FC.LOW.NONSIG                                      1
  FC.NEUTRAL                                         0
               vv
clus            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FC.HIGH.SIG                                                            58
  FC.LOW.NONSIG                                                          63
  FC.NEUTRAL                                                             50
D2V9, multiclass
                                                             clus
vv                                                            FC.HIGH.SIG
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          58
                                                             clus
vv                                                            FC.LOW.NONSIG
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            63
                                                             clus
vv                                                            FC.NEUTRAL
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         50
[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"
D2V10, binary
               cls
clus             0  1
  FC.HIGH.SIG    1 57
  FC.LOW.NONSIG  0 66
  FC.NEUTRAL     4 49
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      1   57
  FC.LOW.NONSIG    0   66
  FC.NEUTRAL       4   49
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO            1             0          4
  YES          57            66         49
[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
D2V12, continuous
               vv
clus            R0 R1 R2 RX
  FC.HIGH.SIG   48  2  2  2
  FC.LOW.NONSIG 56  0  0  4
  FC.NEUTRAL    42  0  2  4
D2V13, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  R0          48            56         42
  R1           2             0          0
  R2           2             0          2
  RX           2             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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG       1                         2    36
  FC.LOW.NONSIG     2                         5    40
  FC.NEUTRAL        2                         2    34
D2V14, multiclass
                           clus
vv                          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ASIAN                               1             2          2
  BLACK OR AFRICAN AMERICAN           2             5          2
  WHITE                              36            40         34
[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.SIG    2 31
  FC.LOW.NONSIG  0 39
  FC.NEUTRAL     1 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      2   31
  FC.LOW.NONSIG    0   39
  FC.NEUTRAL       1   29
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               2             0          1
  NOT HISPANIC OR LATINO          31            39         29
[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"
