[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/22506957/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/LUSC-TP/22526217/APOBEC_clinical_corr_input_22539289/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=504, in cluster file=178, common to both=178
[1]   2 178
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  68   55   55 
   0 HIGH  LOW 
  68   55   55 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            58             52             68 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            58             52             68 
[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] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 178 columns.

[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=83,	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=81,	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=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:'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=51,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'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 178 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] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=37, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
 37 115  14  12 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 37 115  14  12 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 37 115  14  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 37 115  14  12 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
116  39  17   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
116  39  17   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
116  39  17   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
116  39  17   5 
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=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, 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
RESIDUAL_TUMOR, 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    39 27
  HIGH 26 29
  LOW  25 29
   0 HIGH  LOW 
  66   55   54 
   0 HIGH  LOW 
  27   29   29 
$`0`
TCGA-18-3407 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2715 
        4.47        17.88        22.49        18.38        41.42        35.34 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       75.75       117.57        11.34       154.32        49.94       119.54 
TCGA-21-1081 TCGA-21-5786 TCGA-22-1002 TCGA-22-4591 TCGA-22-4599 TCGA-22-4604 
        9.34        33.93         4.31        20.48        38.17        13.12 
TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5492 TCGA-33-4582 
       11.77         0.79        71.34        30.12        16.64       103.53 
TCGA-33-4586 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-37-4133 
       14.07        81.24        74.66        60.30        16.93         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-43-3394 
        6.81         0.39         3.39       126.58       102.18        39.12 
TCGA-43-6647 TCGA-43-6771 TCGA-46-3766 TCGA-46-3767 TCGA-51-4080 TCGA-51-4081 
       24.89         5.46        12.16        13.02         0.39        29.95 
TCGA-56-1622 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 
       28.96        49.48        66.54        42.64        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-66-2734 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 
       26.83        52.67        43.10        21.07         0.92         0.99 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 
       43.99         2.01        23.01         2.01        40.01        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
       10.06         4.01        49.05        12.33         9.67        41.39 

$HIGH
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-33-4532 TCGA-33-6737 
       12.20       123.19         4.80        27.19       129.01        19.76 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-21-1077 TCGA-21-1078 
       23.54        92.15        92.42        86.96        34.78        15.58 
TCGA-21-5782 TCGA-22-1011 TCGA-22-4607 TCGA-22-5473 TCGA-22-5477 TCGA-22-5491 
       31.63         1.74        19.30        63.55        44.25        56.32 
TCGA-33-4547 TCGA-33-4566 TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5928 
       79.53       173.82         2.63        61.61        65.23        39.32 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        4.96         4.01         0.43        55.20        82.52         1.71 
TCGA-39-5031 TCGA-39-5035 TCGA-43-3920 TCGA-46-3765 TCGA-46-3769 TCGA-46-6026 
       60.53        68.38        33.11        13.32         4.44        13.91 
TCGA-51-4079 TCGA-56-5897 TCGA-56-6545 TCGA-60-2698 TCGA-60-2707 TCGA-60-2720 
        0.39        12.43        21.90        10.22        21.93         3.19 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
       21.01        25.05         1.02         2.01        19.00         3.02 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2794 
       19.00        12.00         1.97        25.97         5.03        54.08 
TCGA-85-6561 
       40.24 

$LOW
TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-60-2712 
       31.99         6.18        60.66        64.93       133.74         9.01 
TCGA-60-2721 TCGA-18-3417 TCGA-18-4086 TCGA-21-1071 TCGA-21-1076 TCGA-21-5784 
       32.32        36.07         2.79        46.88        60.89        41.69 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 
       10.82         7.33        14.10        27.02        35.08        24.13 
TCGA-22-4601 TCGA-22-5474 TCGA-22-5482 TCGA-22-5489 TCGA-33-4538 TCGA-33-4583 
       34.75        14.63        11.74        62.86        97.94       151.27 
TCGA-34-2608 TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-39-5019 TCGA-39-5021 
       32.88         9.07        50.66        44.75       111.35        68.58 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-6143 TCGA-43-6770 
       24.33         1.94        71.18        55.56        22.98        21.47 
TCGA-46-3768 TCGA-46-6025 TCGA-56-5898 TCGA-60-2708 TCGA-60-2713 TCGA-60-2722 
        9.83        10.65        18.25        80.45        56.91        29.85 
TCGA-60-2726 TCGA-66-2727 TCGA-66-2744 TCGA-66-2754 TCGA-66-2763 TCGA-66-2767 
       11.77        16.96         0.99         2.01         0.99         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-70-6722 
       12.03         3.98        24.95        22.98         4.04        12.07 

   0 HIGH  LOW 
0.39 0.39 0.99 
     0   HIGH    LOW 
154.32 173.82 151.27 
    0  HIGH   LOW 
24.23 21.90 24.23 
[1] "0.4 - 154.3 (24.2)" "0.4 - 173.8 (21.9)" "1.0 - 151.3 (24.2)"
D1V2, continuous
      vv
clus   STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  0          14       23        10         6          9          5        1
  HIGH       11       22         0        10          6          3        1
  LOW         4       25         3        10          9          3        1
D1V3, multiclass
            clus
vv            0 HIGH LOW
  STAGE IA   14   11   4
  STAGE IB   23   22  25
  STAGE IIA  10    0   3
  STAGE IIB   6   10  10
  STAGE IIIA  9    6   9
  STAGE IIIB  5    3   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
  0    19 36  6  7
  HIGH 11 36  4  4
  LOW   7 43  4  1
D1V4, multiclass
    clus
vv    0 HIGH LOW
  T1 19   11   7
  T2 36   36  43
  T3  6    4   4
  T4  7    4   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
  0    48 15  5  0
  HIGH 36 10  6  2
  LOW  32 14  6  3
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 48   36  32
  N1 15   10  14
  N2  5    6   6
  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    62  1
  HIGH 51  1
  LOW  52  1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      62    1
  HIGH   51    1
  LOW    52    1
   clus
vv   0 HIGH LOW
  0 62   51  52
  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    21 47
  HIGH 13 42
  LOW  13 42
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      21   47
  HIGH   13   42
  LOW    13   42
        clus
vv        0 HIGH LOW
  FEMALE 21   13  13
  MALE   47   42  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"
D1V8, binary
      cls
clus    0  1
  0    46  8
  HIGH 37  6
  LOW  37  6
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      46    8
  HIGH   37    6
  LOW    37    6
     clus
vv     0 HIGH LOW
  NO  46   37  37
  YES  8    6   6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, 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                                                             65
  HIGH                                                          54
  LOW                                                           53
D1V10, 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) 65   54  53
[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"
D1V11, continuous
D1V12, continuous
      vv
clus   R0 R1 R2 RX
  0    57  0  0  4
  HIGH 44  2  2  2
  LOW  46  0  2  4
D1V13, multiclass
    clus
vv    0 HIGH LOW
  R0 57   44  46
  R1  0    2   0
  R2  0    2   2
  RX  4    2   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
  0        2                         5    42
  HIGH     1                         1    35
  LOW      2                         3    36
D1V14, multiclass
                           clus
vv                           0 HIGH LOW
  ASIAN                      2    1   2
  BLACK OR AFRICAN AMERICAN  5    1   3
  WHITE                     42   35  36
[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 41
  HIGH  1 31
  LOW   2 29
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       0   41
  HIGH    1   31
  LOW     2   29
                        clus
vv                        0 HIGH LOW
  HISPANIC OR LATINO      0    1   2
  NOT HISPANIC OR LATINO 41   31  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"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2             0  1
  FC.HIGH.ENRICH 28 30
  FC.LOW.ENRICH  23 28
  FC.NO.ENRICH   39 27
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            58             51             66 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            30             28             27 
$FC.HIGH.ENRICH
TCGA-18-3406 TCGA-18-3410 TCGA-18-5595 TCGA-33-4533 TCGA-33-6737 TCGA-60-2721 
       12.20         4.80        27.19       133.74        19.76        32.32 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
       23.54        92.15        92.42        46.88        60.89        34.78 
TCGA-21-1078 TCGA-21-5782 TCGA-22-1011 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 
       15.58        31.63         1.74        19.30        63.55        14.63 
TCGA-22-5477 TCGA-22-5491 TCGA-33-4547 TCGA-34-2596 TCGA-34-2600 TCGA-34-5928 
       44.25        56.32        79.53         2.63        61.61        39.32 
TCGA-34-5929 TCGA-37-3783 TCGA-37-3789 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        4.96         4.01         0.43        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 TCGA-43-3920 TCGA-46-3765 TCGA-46-3769 
       24.33        60.53        68.38        33.11        13.32         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-56-5897 TCGA-56-6545 TCGA-60-2698 
       10.65        13.91         0.39        12.43        21.90        10.22 
TCGA-60-2707 TCGA-60-2720 TCGA-60-2726 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
       21.93         3.19        11.77        21.01        25.05         1.02 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 
        2.01        19.00         3.02        19.00        12.00         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2791 TCGA-66-2794 
       25.97        22.98         5.03        54.08 

$FC.LOW.ENRICH
TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
      123.19        31.99         6.18        60.66        64.93       129.01 
TCGA-60-2712 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-21-5784 TCGA-21-5787 
        9.01        36.07        86.96         2.79        41.69        10.82 
TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 
        7.33        14.10        27.02        35.08        24.13        34.75 
TCGA-22-5482 TCGA-22-5489 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-34-2608 
       11.74        62.86        97.94       173.82       151.27        32.88 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-39-5019 TCGA-39-5021 
       65.23         9.07        50.66        44.75       111.35        68.58 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-6143 TCGA-43-6770 TCGA-46-3768 
        1.94        71.18        55.56        22.98        21.47         9.83 
TCGA-56-5898 TCGA-60-2708 TCGA-60-2713 TCGA-60-2722 TCGA-66-2727 TCGA-66-2744 
       18.25        80.45        56.91        29.85        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-66-2789 TCGA-70-6722 TCGA-85-6561 
        4.04        12.07        40.24 

$FC.NO.ENRICH
TCGA-18-3407 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-60-2711 TCGA-60-2715 
        4.47        17.88        22.49        18.38        41.42        35.34 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       75.75       117.57        11.34       154.32        49.94       119.54 
TCGA-21-1081 TCGA-21-5786 TCGA-22-1002 TCGA-22-4591 TCGA-22-4599 TCGA-22-4604 
        9.34        33.93         4.31        20.48        38.17        13.12 
TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5485 TCGA-22-5492 TCGA-33-4582 
       11.77         0.79        71.34        30.12        16.64       103.53 
TCGA-33-4586 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-37-4133 
       14.07        81.24        74.66        60.30        16.93         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-43-3394 
        6.81         0.39         3.39       126.58       102.18        39.12 
TCGA-43-6647 TCGA-43-6771 TCGA-46-3766 TCGA-46-3767 TCGA-51-4080 TCGA-51-4081 
       24.89         5.46        12.16        13.02         0.39        29.95 
TCGA-56-1622 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 
       28.96        49.48        66.54        42.64        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-66-2734 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 
       26.83        52.67        43.10        21.07         0.92         0.99 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 
       43.99         2.01        23.01         2.01        40.01        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-70-6723 TCGA-85-6175 TCGA-85-6560 
       10.06         4.01        49.05        12.33         9.67        41.39 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.39           0.99           0.39 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        133.74         173.82         154.32 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        20.385         29.850         24.230 
[1] "0.4 - 133.7 (20.4)" "1.0 - 173.8 (29.9)" "0.4 - 154.3 (24.2)"
D2V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  FC.HIGH.ENRICH        9       24         1        11          7          3
  FC.LOW.ENRICH         6       23         2         9          8          3
  FC.NO.ENRICH         14       23        10         6          9          5
                vv
clus             STAGE IV
  FC.HIGH.ENRICH        1
  FC.LOW.ENRICH         1
  FC.NO.ENRICH          1
D2V3, multiclass
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE IA                9             6           14
  STAGE IB               24            23           23
  STAGE IIA               1             2           10
  STAGE IIB              11             9            6
  STAGE IIIA              7             8            9
  STAGE IIIB              3             3            5
  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.ENRICH 10 40  4  4
  FC.LOW.ENRICH   8 39  4  1
  FC.NO.ENRICH   19 36  6  7
D2V4, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T1             10             8           19
  T2             40            39           36
  T3              4             4            6
  T4              4             1            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             N0 N1 N2 N3
  FC.HIGH.ENRICH 37 12  7  2
  FC.LOW.ENRICH  31 12  5  3
  FC.NO.ENRICH   48 15  5  0
D2V5, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0             37            31           48
  N1             12            12           15
  N2              7             5            5
  N3              2             3            0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 54  1
  FC.LOW.ENRICH  49  1
  FC.NO.ENRICH   62  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   54    1
  FC.LOW.ENRICH    49    1
  FC.NO.ENRICH     62    1
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0             54            49           62
  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.ENRICH 15 43
  FC.LOW.ENRICH  11 41
  FC.NO.ENRICH   21 47
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   15   43
  FC.LOW.ENRICH    11   41
  FC.NO.ENRICH     21   47
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE             15            11           21
  MALE               43            41           47
[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 42  5
  FC.LOW.ENRICH  32  7
  FC.NO.ENRICH   46  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   42    5
  FC.LOW.ENRICH    32    7
  FC.NO.ENRICH     46    8
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO              42            32           46
  YES              5             7            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"
D2V9, continuous
                vv
clus             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  FC.HIGH.ENRICH                                     0
  FC.LOW.ENRICH                                      3
  FC.NO.ENRICH                                       2
                vv
clus             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  FC.HIGH.ENRICH                                      0
  FC.LOW.ENRICH                                       0
  FC.NO.ENRICH                                        1
                vv
clus             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FC.HIGH.ENRICH                                                          58
  FC.LOW.ENRICH                                                           49
  FC.NO.ENRICH                                                            65
D2V10, multiclass
                                                             clus
vv                                                            FC.HIGH.ENRICH
  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.ENRICH
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            49
                                                             clus
vv                                                            FC.NO.ENRICH
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           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"
D2V11, continuous
D2V12, continuous
                vv
clus             R0 R1 R2 RX
  FC.HIGH.ENRICH 48  2  2  2
  FC.LOW.ENRICH  42  0  2  4
  FC.NO.ENRICH   57  0  0  4
D2V13, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  R0             48            42           57
  R1              2             0            0
  R2              2             2            0
  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.ENRICH     1                         2    36
  FC.LOW.ENRICH      2                         2    35
  FC.NO.ENRICH       2                         5    42
D2V14, multiclass
                           clus
vv                          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ASIAN                                  1             2            2
  BLACK OR AFRICAN AMERICAN              2             2            5
  WHITE                                 36            35           42
[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  2 31
  FC.LOW.ENRICH   1 29
  FC.NO.ENRICH    0 41
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    2   31
  FC.LOW.ENRICH     1   29
  FC.NO.ENRICH      0   41
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  2             1            0
  NOT HISPANIC OR LATINO             31            29           41
[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"
