[1] "ofn"        "-oTLUAD-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/LUAD-TP/22506767/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/LUAD-TP/22552622/__DELETED__1436046:APOBEC_clinical_corr_input_22572022/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=522, in cluster file=533, common to both=481
[1]   2 481
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 265  113  103 
   0 HIGH  LOW 
 265  113  103 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           147             69            265 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           147             69            265 
[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 481 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=163,	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=268,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	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=5,	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=22,	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=4,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=90,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	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 481 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=49, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
156 261  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
156 261  43  18 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
156 261  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
156 261  43  18 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
308  89  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  308    89    72 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
308  89  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  308    89    72 
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=11, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=90, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=57, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2    0   1
  0    174  85
  HIGH  64  46
  LOW   60  40
   0 HIGH  LOW 
 259  110  100 
   0 HIGH  LOW 
  85   46   40 
$`0`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96        20.05         9.01        15.02        15.02 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7671 
       11.64        14.73        38.10        23.93        86.01        29.23 
TCGA-44-8119 TCGA-49-4501 TCGA-50-5932 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
        9.37        46.72        40.60        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 
       16.01        14.53        19.66        19.73        17.98        32.12 
TCGA-55-8619 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       13.68        19.59        13.87        82.68        39.09         8.48 
TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7562 
       50.24        85.32        13.71         1.45        16.54         2.86 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 
       21.40        17.92        20.19        20.52        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       10.09        37.02        19.00         2.99        14.96        29.98 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5429 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        9.04         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 
       44.61         4.37        46.98        28.01        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 
       21.63        23.18        61.28        16.44        22.72        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       18.87        23.64        12.66         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       11.54        13.45        35.54        32.84        29.46        29.75 
TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       55.33        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 
       49.28         9.27        14.27        78.67        60.72        57.53 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        3.91        11.05         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       27.25        13.94        35.21        14.30        80.52        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 
       15.25        46.03         3.88        69.34        45.34        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7576 TCGA-55-7728 
       24.99        40.54       107.21        31.30        22.03        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 
       25.41        15.39        34.19        15.19        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       15.65        29.19        15.42        15.72         0.36        13.74 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       20.28        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
        1.58        12.33        21.40        15.81        19.99        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       42.38        14.60        49.25        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-5774 
       72.30        13.61        39.25        29.92        56.81        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
        2.04        28.41        28.47        18.84        14.04        14.73 
TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
        5.72         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-8254 TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4668 
        6.05        13.45         8.42         6.90        23.38        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 
        4.31        30.31         9.24         1.25        77.85        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 
       49.84       108.66       100.57        27.16        20.58        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 
       22.92         9.57       238.29        31.20         8.02        39.35 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
       39.75        77.59        93.11        31.13        38.04        20.55 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       32.78        37.74         4.08         0.79        22.82        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4P8 
       23.05        21.47        14.60        13.91        30.84        26.47 
TCGA-91-6831 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       10.19        27.68         1.15        16.60        14.27        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7567 TCGA-95-A4VP TCGA-97-7546 
       17.46        23.61         1.08        18.67        19.89        42.25 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
       63.52        61.48        25.48        18.54        18.67        18.12 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       14.30        20.58        19.76        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4SW 
        1.45        21.57        32.48        19.00        14.30        58.45 
TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       49.35         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91        71.05        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

$HIGH
TCGA-05-4382 TCGA-05-4402 TCGA-38-4630 TCGA-38-7271 TCGA-44-7661 TCGA-44-7670 
       19.96         8.02        35.28        26.30        18.31        29.00 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5935 TCGA-55-6979 TCGA-55-7726 
       16.04        17.16        11.64        21.47         7.79        21.44 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       16.93        19.69        18.15        20.19        20.65        52.60 
TCGA-93-8067 TCGA-95-7947 TCGA-95-7948 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 
        6.12        15.68        15.65        45.01         0.00        24.03 
TCGA-05-4398 TCGA-05-4424 TCGA-05-5428 TCGA-05-5715 TCGA-38-4625 TCGA-44-3396 
       47.05        30.02        22.03         2.04        97.74        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-6777 TCGA-44-7662 TCGA-44-A47A 
       38.24        34.06        33.73        32.45         7.17        15.32 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4514 TCGA-49-6743 TCGA-50-5044 
       13.64        76.21        28.11        55.89        53.29        20.52 
TCGA-50-5936 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-53-7624 TCGA-55-5899 
        8.45        53.16        42.35        25.55        34.29        30.58 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6982 TCGA-55-6987 TCGA-55-7570 
        5.62        42.51        53.65        32.71        70.26        27.09 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7907 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
       32.71         3.91        11.28        29.23        29.72        23.08 
TCGA-55-8092 TCGA-55-8208 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-62-8399 
        5.06        22.16        20.71         3.25         0.92        88.64 
TCGA-62-A46O TCGA-62-A471 TCGA-64-5781 TCGA-67-3771 TCGA-69-7765 TCGA-69-7978 
       47.80        40.96        51.25        20.05         5.42         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-75-6214 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 
       13.41        13.51        36.66         5.69       129.53        21.90 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7220 TCGA-78-7539 
       39.95        19.50        38.50        32.09        26.53        26.01 
TCGA-78-8640 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-8056 TCGA-86-8073 
      232.18       110.50        27.09         5.88         4.57        24.33 
TCGA-86-8278 TCGA-86-8585 TCGA-86-A4JF TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 
       31.04        11.61        24.23         1.97        12.23         7.36 
TCGA-91-8499 TCGA-95-7944 TCGA-95-8494 TCGA-97-7547 TCGA-97-8176 TCGA-97-A4M0 
        1.18        12.39         2.76        64.60        15.39        21.44 
TCGA-97-A4M5 TCGA-99-8025 TCGA-J2-A4AD TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TI 
       20.84        34.85        18.08        38.63        86.14        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YP 
       19.13         1.64 

$LOW
TCGA-05-4427 TCGA-38-4629 TCGA-44-6147 TCGA-44-A47F TCGA-50-6597 TCGA-55-1592 
       26.01        28.41        27.78        11.08        41.69        23.05 
TCGA-55-7724 TCGA-55-7914 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-78-8660 
       23.18         6.15        16.93        22.65        20.58        10.55 
TCGA-91-7771 TCGA-93-A4JQ TCGA-95-A4VN TCGA-97-A4M3 TCGA-MP-A4TC TCGA-05-4249 
       16.18        17.29        18.18        17.75         2.43        50.07 
TCGA-05-4250 TCGA-05-4422 TCGA-05-5425 TCGA-35-4122 TCGA-44-2657 TCGA-44-2665 
        3.98        12.00        29.00         7.40        44.42        42.77 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-7660 TCGA-49-4488 
       26.56        33.30        28.37        23.77        19.46        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6767 TCGA-50-5072 TCGA-50-5939 
       12.66        14.07         8.81        22.26         8.22        15.12 
TCGA-50-5941 TCGA-50-6594 TCGA-50-6595 TCGA-53-7626 TCGA-55-7281 TCGA-55-7283 
       48.46        12.16         6.21        30.54        28.67        20.02 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8301 TCGA-55-8505 
       18.64        17.65        18.44        19.82        17.56        14.47 
TCGA-55-8510 TCGA-62-8394 TCGA-62-A46R TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
       17.72         4.57        56.71        81.80        38.37        42.90 
TCGA-67-6216 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-7499 
        4.64        14.01         4.24        19.43        26.30        50.33 
TCGA-75-5125 TCGA-75-5147 TCGA-78-7143 TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 
       66.64        43.82       163.10        19.27       119.51         5.88 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7542 TCGA-86-6562 TCGA-86-7711 
      104.19        88.14        53.33        10.55        12.36        34.39 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8076 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       19.89        35.24        32.65        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
       26.50        29.46        13.64        10.62        41.36         2.60 
TCGA-93-7347 TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-97-7938 TCGA-97-7941 
       22.45        19.00        41.82        27.29         0.59        15.91 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-J2-A4AE TCGA-MN-A4N5 TCGA-MP-A4T2 
        5.39        16.41        21.60        35.47         2.76        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       86.04        58.85        74.33         0.13 

   0 HIGH  LOW 
0.36 0.00 0.13 
     0   HIGH    LOW 
238.29 232.18 163.10 
     0   HIGH    LOW 
21.400 21.965 21.090 
[1] "0.4 - 238.3 (21.4)" "0.0 - 232.2 (22.0)" "0.1 - 163.1 (21.1)"
D1V2, continuous
      vv
clus   STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  0          3       64       73        23        37         38          5
  HIGH       1       28       31        14        12         17          4
  LOW        0       29       28         9        17         15          2
      vv
clus   STAGE IV
  0          17
  HIGH        4
  LOW         3
D1V3, multiclass
            clus
vv            0 HIGH LOW
  STAGE I     3    1   0
  STAGE IA   64   28  29
  STAGE IB   73   31  28
  STAGE IIA  23   14   9
  STAGE IIB  37   12  17
  STAGE IIIA 38   17  15
  STAGE IIIB  5    4   2
  STAGE IV   17    4   3
[1] 8 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     80 150  24   9
  HIGH  39  60   7   7
  LOW   37  51  12   2
D1V4, multiclass
    clus
vv     0 HIGH LOW
  T1  80   39  37
  T2 150   60  51
  T3  24    7  12
  T4   9    7   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    173  46    40
  HIGH  71  23    17
  LOW   64  20    15
D1V5, multiclass
       clus
vv        0 HIGH LOW
  N0    173   71  64
  N1     46   23  20
  N2+N3  40   17  15
[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"
D1V6, binary
      cls
clus     0   1
  0    173  16
  HIGH  83   4
  LOW   72   3
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     173   16
  HIGH   83    4
  LOW    72    3
   clus
vv    0 HIGH LOW
  0 173   83  72
  1  16    4   3
[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    141 124
  HIGH  60  53
  LOW   59  44
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     141  124
  HIGH   60   53
  LOW    59   44
        clus
vv         0 HIGH LOW
  FEMALE 141   60  59
  MALE   124   53  44
[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    205  34
  HIGH  91  12
  LOW   88   9
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     205   34
  HIGH   91   12
  LOW    88    9
     clus
vv      0 HIGH LOW
  NO  205   91  88
  YES  34   12   9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
      vv
clus   LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  0                            12                                59
  HIGH                          2                                26
  LOW                           3                                17
      vv
clus   LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  0                                                   158
  HIGH                                                 72
  LOW                                                  66
      vv
clus   LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  0                                             4
  HIGH                                          0
  LOW                                           0
      vv
clus   LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  0                                               11
  HIGH                                             1
  LOW                                              7
      vv
clus   LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  0                                 1                                  3
  HIGH                              1                                  0
  LOW                               0                                  0
      vv
clus   LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  0                               2                             6
  HIGH                            0                             8
  LOW                             0                             8
      vv
clus   LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  0                                                2
  HIGH                                             1
  LOW                                              2
      vv
clus   MUCINOUS (COLLOID) CARCINOMA
  0                               7
  HIGH                            2
  LOW                             0
D1V10, multiclass
                                                    clus
vv                                                     0 HIGH LOW
  LUNG ACINAR ADENOCARCINOMA                          12    2   3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                   59   26  17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 158   72  66
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS           4    0   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS       11    1   7
  LUNG CLEAR CELL ADENOCARCINOMA                       1    1   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                   3    0   0
  LUNG MUCINOUS ADENOCARCINOMA                         2    0   0
  LUNG PAPILLARY ADENOCARCINOMA                        6    8   8
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA        2    1   2
  MUCINOUS (COLLOID) CARCINOMA                         7    2   0
[1] 11  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    166   7   1  17
  HIGH  74   4   2   3
  LOW   72   1   1   5
D1V13, multiclass
    clus
vv     0 HIGH LOW
  R0 166   74  72
  R1   7    4   1
  R2   1    2   1
  RX  17    3   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   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1     4                        21   203
  HIGH                                0     1                         4    91
  LOW                                 0     2                         5    84
D1V14, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   0
  ASIAN                              4    1   2
  BLACK OR AFRICAN AMERICAN         21    4   5
  WHITE                            203   91  84
[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"
D1V15, binary
      cls
clus     0   1
  0      2 198
  HIGH   2  77
  LOW    2  76
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       2  198
  HIGH    2   77
  LOW     2   76
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       2    2   2
  NOT HISPANIC OR LATINO 198   77  76
[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  82  61
  FC.LOW.ENRICH   42  25
  FC.NO.ENRICH   174  85
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           143             67            259 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            61             25             85 
$FC.HIGH.ENRICH
TCGA-05-4382 TCGA-05-4402 TCGA-38-4630 TCGA-38-7271 TCGA-44-6147 TCGA-44-7661 
       19.96         8.02        35.28        26.30        27.78        18.31 
TCGA-44-7670 TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5935 
       29.00        11.08        16.04        17.16        11.64        21.47 
TCGA-55-6979 TCGA-55-7726 TCGA-55-8204 TCGA-55-8205 TCGA-55-8621 TCGA-55-A4DF 
        7.79        21.44        16.93        19.69        16.93        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-78-8660 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 
       20.65        52.60        10.55         6.12        17.29        15.68 
TCGA-95-7948 TCGA-97-A4M3 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       15.65        17.75        45.01         0.00        24.03        47.05 
TCGA-05-4422 TCGA-05-4424 TCGA-05-5428 TCGA-05-5715 TCGA-38-4625 TCGA-44-2665 
       12.00        30.02        22.03         2.04        97.74        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-6777 TCGA-44-A47A TCGA-49-4486 
       37.15        38.24        33.73        32.45        15.32        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 
       28.11        28.57        12.66         8.81        55.89        53.29 
TCGA-50-5044 TCGA-50-5936 TCGA-50-5939 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       20.52         8.45        15.12        53.16        42.35        25.55 
TCGA-53-7624 TCGA-55-5899 TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6982 
       34.29        30.58         5.62        42.51        53.65        32.71 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7907 TCGA-55-7995 
       70.26        27.09        32.71         3.91        11.28        29.23 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8208 TCGA-55-8505 TCGA-55-A48Y 
       29.72        23.08         5.06        22.16        14.47        20.71 
TCGA-55-A493 TCGA-62-8394 TCGA-62-8399 TCGA-62-A46O TCGA-62-A471 TCGA-64-1681 
        0.92         4.57        88.64        47.80        40.96        38.37 
TCGA-67-3771 TCGA-67-6216 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       20.05         4.64         5.42         4.41        13.51        14.01 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 TCGA-78-7146 
       50.33        66.64        43.82        36.66       163.10         5.69 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
      129.53        21.90        39.95       119.51        19.50        32.09 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 
        5.88       104.19        88.14        26.53        26.01        10.55 
TCGA-78-8640 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7954 
      232.18        27.09        12.36         5.88        34.39        19.89 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8671 TCGA-86-8674 
        4.57        32.65        31.04        11.61        27.58        26.50 
TCGA-86-A4P7 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 
       13.64         1.97         2.60        12.23         7.36         1.18 
TCGA-93-7347 TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 
       22.45        19.00        12.39        27.29         2.76        64.60 
TCGA-97-7938 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 
        0.59        15.39        16.41        21.60        21.44        20.84 
TCGA-99-8025 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 
       34.85        18.08        35.47        38.63        86.14        37.35 
TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YP 
       58.85        14.10        19.13        74.33         1.64 

$FC.LOW.ENRICH
TCGA-05-4427 TCGA-38-4629 TCGA-50-6597 TCGA-55-1592 TCGA-55-7724 TCGA-55-7914 
       26.01        28.41        41.69        23.05        23.18         6.15 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-91-7771 TCGA-95-A4VN TCGA-MP-A4TC 
       18.15        22.65        20.58        16.18        18.18         2.43 
TCGA-05-4249 TCGA-05-4250 TCGA-05-5425 TCGA-35-4122 TCGA-44-2657 TCGA-44-3918 
       50.07         3.98        29.00         7.40        44.42        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-7660 TCGA-44-7662 
       26.56        33.30        28.37        23.77        19.46         7.17 
TCGA-44-A4SS TCGA-49-4505 TCGA-49-6767 TCGA-50-5072 TCGA-50-5941 TCGA-50-6594 
       13.64        14.07        22.26         8.22        48.46        12.16 
TCGA-50-6595 TCGA-53-7626 TCGA-55-7281 TCGA-55-7283 TCGA-55-7903 TCGA-55-7911 
        6.21        30.54        28.67        20.02        18.64        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8301 TCGA-55-8510 TCGA-55-A490 TCGA-62-A46R 
       18.44        19.82        17.56        17.72         3.25        56.71 
TCGA-64-1679 TCGA-64-5778 TCGA-64-5781 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
       81.80        42.90        51.25        13.41         4.24        19.43 
TCGA-73-4666 TCGA-78-7147 TCGA-78-7155 TCGA-78-7537 TCGA-78-8662 TCGA-86-7955 
       26.30        19.27        38.50        53.33       110.50        35.24 
TCGA-86-8073 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-91-6828 
       24.33         0.62        28.34        29.46        24.23        10.62 
TCGA-91-6829 TCGA-95-7039 TCGA-97-7941 TCGA-97-8174 TCGA-MN-A4N5 TCGA-MP-A4T4 
       41.36        41.82        15.91         5.39         2.76        86.04 
TCGA-NJ-A4YI 
        0.13 

$FC.NO.ENRICH
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96        20.05         9.01        15.02        15.02 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7671 
       11.64        14.73        38.10        23.93        86.01        29.23 
TCGA-44-8119 TCGA-49-4501 TCGA-50-5932 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
        9.37        46.72        40.60        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 
       16.01        14.53        19.66        19.73        17.98        32.12 
TCGA-55-8619 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       13.68        19.59        13.87        82.68        39.09         8.48 
TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7562 
       50.24        85.32        13.71         1.45        16.54         2.86 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 
       21.40        17.92        20.19        20.52        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       10.09        37.02        19.00         2.99        14.96        29.98 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5429 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        9.04         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 
       44.61         4.37        46.98        28.01        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 
       21.63        23.18        61.28        16.44        22.72        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       18.87        23.64        12.66         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       11.54        13.45        35.54        32.84        29.46        29.75 
TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       55.33        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 
       49.28         9.27        14.27        78.67        60.72        57.53 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        3.91        11.05         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       27.25        13.94        35.21        14.30        80.52        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 
       15.25        46.03         3.88        69.34        45.34        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7576 TCGA-55-7728 
       24.99        40.54       107.21        31.30        22.03        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 
       25.41        15.39        34.19        15.19        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       15.65        29.19        15.42        15.72         0.36        13.74 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       20.28        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
        1.58        12.33        21.40        15.81        19.99        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       42.38        14.60        49.25        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-5774 
       72.30        13.61        39.25        29.92        56.81        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
        2.04        28.41        28.47        18.84        14.04        14.73 
TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
        5.72         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-8254 TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4668 
        6.05        13.45         8.42         6.90        23.38        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 
        4.31        30.31         9.24         1.25        77.85        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 
       49.84       108.66       100.57        27.16        20.58        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 
       22.92         9.57       238.29        31.20         8.02        39.35 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
       39.75        77.59        93.11        31.13        38.04        20.55 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       32.78        37.74         4.08         0.79        22.82        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4P8 
       23.05        21.47        14.60        13.91        30.84        26.47 
TCGA-91-6831 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       10.19        27.68         1.15        16.60        14.27        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7567 TCGA-95-A4VP TCGA-97-7546 
       17.46        23.61         1.08        18.67        19.89        42.25 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
       63.52        61.48        25.48        18.54        18.67        18.12 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       14.30        20.58        19.76        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4SW 
        1.45        21.57        32.48        19.00        14.30        58.45 
TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       49.35         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91        71.05        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.00           0.13           0.36 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        232.18         110.50         238.29 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         21.60          22.26          21.40 
[1] "0.0 - 232.2 (21.6)" "0.1 - 110.5 (22.3)" "0.4 - 238.3 (21.4)"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FC.HIGH.ENRICH       1       42       35        17        16         22
  FC.LOW.ENRICH        0       15       24         6        13         10
  FC.NO.ENRICH         3       64       73        23        37         38
                vv
clus             STAGE IIIB STAGE IV
  FC.HIGH.ENRICH          6        6
  FC.LOW.ENRICH           0        1
  FC.NO.ENRICH            5       17
D2V3, multiclass
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                 1             0            3
  STAGE IA               42            15           64
  STAGE IB               35            24           73
  STAGE IIA              17             6           23
  STAGE IIB              16            13           37
  STAGE IIIA             22            10           38
  STAGE IIIB              6             0            5
  STAGE IV                6             1           17
[1] 8 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  56  73   8   9
  FC.LOW.ENRICH   20  38  11   0
  FC.NO.ENRICH    80 150  24   9
D2V4, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T1             56            20           80
  T2             73            38          150
  T3              8            11           24
  T4              9             0            9
[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  86  33    23
  FC.LOW.ENRICH   49  10     9
  FC.NO.ENRICH   173  46    40
D2V5, multiclass
       clus
vv      FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0                86            49          173
  N1                33            10           46
  N2+N3             23             9           40
[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"
D2V6, binary
                cls
clus               0   1
  FC.HIGH.ENRICH 108   6
  FC.LOW.ENRICH   47   1
  FC.NO.ENRICH   173  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  108    6
  FC.LOW.ENRICH    47    1
  FC.NO.ENRICH    173   16
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0            108            47          173
  1              6             1           16
[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  81  66
  FC.LOW.ENRICH   38  31
  FC.NO.ENRICH   141 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   81   66
  FC.LOW.ENRICH    38   31
  FC.NO.ENRICH    141  124
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE             81            38          141
  MALE               66            31          124
[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 121  15
  FC.LOW.ENRICH   58   6
  FC.NO.ENRICH   205  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  121   15
  FC.LOW.ENRICH    58    6
  FC.NO.ENRICH    205   34
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO             121            58          205
  YES             15             6           34
[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 ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FC.HIGH.ENRICH                          3                                36
  FC.LOW.ENRICH                           2                                 7
  FC.NO.ENRICH                           12                                59
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FC.HIGH.ENRICH                                                 88
  FC.LOW.ENRICH                                                  50
  FC.NO.ENRICH                                                  158
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FC.HIGH.ENRICH                                          0
  FC.LOW.ENRICH                                           0
  FC.NO.ENRICH                                            4
                vv
clus             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FC.HIGH.ENRICH                                             3
  FC.LOW.ENRICH                                              5
  FC.NO.ENRICH                                              11
                vv
clus             LUNG CLEAR CELL ADENOCARCINOMA
  FC.HIGH.ENRICH                              1
  FC.LOW.ENRICH                               0
  FC.NO.ENRICH                                1
                vv
clus             LUNG MICROPAPILLARY ADENOCARCINOMA
  FC.HIGH.ENRICH                                  0
  FC.LOW.ENRICH                                   0
  FC.NO.ENRICH                                    3
                vv
clus             LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  FC.HIGH.ENRICH                            0                            13
  FC.LOW.ENRICH                             0                             3
  FC.NO.ENRICH                              2                             6
                vv
clus             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FC.HIGH.ENRICH                                             1
  FC.LOW.ENRICH                                              2
  FC.NO.ENRICH                                               2
                vv
clus             MUCINOUS (COLLOID) CARCINOMA
  FC.HIGH.ENRICH                            2
  FC.LOW.ENRICH                             0
  FC.NO.ENRICH                              7
D2V10, multiclass
                                                    clus
vv                                                   FC.HIGH.ENRICH
  LUNG ACINAR ADENOCARCINOMA                                      3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   3
  LUNG CLEAR CELL ADENOCARCINOMA                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                              0
  LUNG MUCINOUS ADENOCARCINOMA                                    0
  LUNG PAPILLARY ADENOCARCINOMA                                  13
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                   1
  MUCINOUS (COLLOID) CARCINOMA                                    2
                                                    clus
vv                                                   FC.LOW.ENRICH FC.NO.ENRICH
  LUNG ACINAR ADENOCARCINOMA                                     2           12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              7           59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            50          158
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                     0            4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  5           11
  LUNG CLEAR CELL ADENOCARCINOMA                                 0            1
  LUNG MICROPAPILLARY ADENOCARCINOMA                             0            3
  LUNG MUCINOUS ADENOCARCINOMA                                   0            2
  LUNG PAPILLARY ADENOCARCINOMA                                  3            6
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                  2            2
  MUCINOUS (COLLOID) CARCINOMA                                   0            7
[1] 11  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  98   5   2   5
  FC.LOW.ENRICH   48   0   1   3
  FC.NO.ENRICH   166   7   1  17
D2V13, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  R0             98            48          166
  R1              5             0            7
  R2              2             1            1
  RX              5             3           17
[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             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.ENRICH                                0     2
  FC.LOW.ENRICH                                 0     1
  FC.NO.ENRICH                                  1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH                         5   119
  FC.LOW.ENRICH                          4    56
  FC.NO.ENRICH                          21   203
D2V14, multiclass
                                  clus
vv                                 FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE              0             0            1
  ASIAN                                         2             1            4
  BLACK OR AFRICAN AMERICAN                     5             4           21
  WHITE                                       119            56          203
[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"
D2V15, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   3 100
  FC.LOW.ENRICH    1  53
  FC.NO.ENRICH     2 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    3  100
  FC.LOW.ENRICH     1   53
  FC.NO.ENRICH      2  198
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  3             1            2
  NOT HISPANIC OR LATINO            100            53          198
[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"
