[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/15084450/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/LUAD-TP/15246504/APOBEC_clinical_corr_input_15246553/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=521, in cluster file=533, common to both=480
[1]   2 480
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 268  132   80 
   0 HIGH  LOW 
 268  132   80 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          148           263            69 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          148           263            69 
[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 480 columns.

[1] "Batch" "23"   
[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=134,	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=300,	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=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:'DCC_UPLOAD_DATE':	nDistinctValues=6,	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=22,	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=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	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=11,	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=91,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=25,	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 480 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=49, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
155 261  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
155 261  43  18 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
155 261  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
155 261  43  18 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
307  89  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  307    89    72 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
307  89  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  307    89    72 
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=11, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=91, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=57, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, 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    183  71
  HIGH  83  44
  LOW   49  26
   0 HIGH  LOW 
 254  127   75 
   0 HIGH  LOW 
  71   44   26 
$`0`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       14.01        37.02         9.96        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96         9.01        29.98        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 
       25.02        24.00        15.02        15.02         9.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 
        5.98         8.68       120.79        37.71        49.05        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-5645 
       44.61        14.73         4.37        46.98        24.36        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       61.28        16.44        14.60        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       23.64        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       11.54        13.45        35.54        46.72        32.84        29.46 
TCGA-49-4512 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       29.75        29.26        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         9.27        14.27        40.60        78.67 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 
       29.03        25.12         3.91        11.05        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        25.61         7.59        27.25        13.94         9.21 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       48.62         0.07        32.65        40.73        15.25         0.82 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
        3.88         5.49         2.20        45.34        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7284 TCGA-55-7573 TCGA-55-7576 
       40.54       107.21         1.74         7.99         0.13         1.32 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-7914 
        1.28         0.79         1.78         1.45         6.48         6.15 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        19.66        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
       17.98         1.51         2.17        15.42         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.36         0.26         0.49         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48Z 
       17.62         0.49         1.58         1.61         2.17        21.40 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       19.59        15.81        19.99        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       49.25        19.53        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       39.25        29.92        56.81        87.98         2.04        28.41 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
       28.47        18.84        14.04         5.72        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 
        6.12        22.68        13.61         7.56         6.05        13.45 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
        2.01         0.10        23.38        29.98        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 TCGA-78-7148 
        1.32         5.39         1.25        39.09        27.16        20.58 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
       64.90        22.29         7.07       223.96         8.48        31.20 
TCGA-78-7536 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-86-7701 
        8.02        39.35        32.68        39.75        77.59        31.13 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
       13.87        20.55        19.43        24.49         4.08         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       15.75        15.85        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 
       30.84        26.47        10.19        13.71        27.68         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27         1.45        19.82         4.18        23.61 
TCGA-93-A4JO TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-A4VK TCGA-95-A4VP 
        1.08         1.22         2.86        18.67        21.40        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
       31.69        63.52        43.79        25.48         5.95        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       17.92        18.12        14.30        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.52        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        5.59        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T7 
       14.30         3.81         0.20        27.19        58.45         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       14.66        73.91        71.05        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

$HIGH
TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       19.96        45.01         0.00        24.03        47.05         8.02 
TCGA-05-4424 TCGA-05-4427 TCGA-05-5428 TCGA-05-5715 TCGA-38-4625 TCGA-38-4630 
       30.02        26.01        22.03         2.04        97.74        35.28 
TCGA-38-7271 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-6777 
       26.30        37.15        38.24        34.06         6.25        32.45 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A4SS TCGA-49-4486 
       12.03         7.17        29.00        15.32        13.64        76.21 
TCGA-49-4487 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       28.11         8.81        55.89        14.63        12.13        17.16 
TCGA-49-6761 TCGA-50-5044 TCGA-50-5935 TCGA-50-5936 TCGA-50-5946 TCGA-50-6590 
       11.64        20.52        21.47         8.45        22.55        42.35 
TCGA-50-6592 TCGA-50-6594 TCGA-53-7624 TCGA-55-1592 TCGA-55-5899 TCGA-55-6712 
       25.55        12.16        34.29        23.05         2.86         0.79 
TCGA-55-6968 TCGA-55-6972 TCGA-55-6979 TCGA-55-6982 TCGA-55-6987 TCGA-55-7283 
       42.51        48.49         7.79        32.71        70.26         1.15 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 TCGA-55-7994 
        0.20         3.12         1.28         1.12         0.53        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8205 TCGA-55-8208 
        0.16        29.72         3.29         5.06         1.08        22.16 
TCGA-55-8511 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8394 
        0.30        20.71         1.58         0.92        20.19         4.57 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A471 TCGA-64-1677 TCGA-64-5781 TCGA-67-3771 
       88.64        47.80        40.96        20.65        51.25        20.05 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-73-4658 
        5.42         2.30         2.93        12.56         7.04        52.60 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        5.69        19.27        35.93        21.90        39.52        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 
       38.50        32.09         5.88        26.53        10.75        10.55 
TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-8056 
      214.62        10.55       110.50        27.09         5.88         4.57 
TCGA-86-8073 TCGA-86-8278 TCGA-86-8585 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       24.33        15.65         1.15        14.96        13.32        17.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-8067 
       41.36         1.97        12.23         7.36         1.18         6.12 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 
       17.29         1.12        12.39        15.68        15.65         2.76 
TCGA-97-7547 TCGA-97-7938 TCGA-97-8176 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8025 
       64.60         0.59        15.39        21.44        20.84        34.85 
TCGA-J2-A4AD TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4TI TCGA-MP-A4TK 
       18.08        38.63         2.76        86.14        14.10        19.13 
TCGA-NJ-A4YP 
        1.64 

$LOW
TCGA-05-4249 TCGA-05-4250 TCGA-05-4422 TCGA-05-5423 TCGA-05-5425 TCGA-38-4629 
       50.07         3.98        12.00         4.96        29.00        28.41 
TCGA-44-2657 TCGA-44-2665 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       13.15        42.77        26.56        33.30        28.37        23.77 
TCGA-44-6147 TCGA-44-7660 TCGA-44-A47F TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       27.78        19.46        11.08        28.57        12.66        14.07 
TCGA-49-6767 TCGA-50-5072 TCGA-50-5939 TCGA-50-5941 TCGA-50-6595 TCGA-53-7626 
       22.26         8.22        15.12        18.64         6.21        30.54 
TCGA-55-7281 TCGA-55-7724 TCGA-55-7903 TCGA-55-7911 TCGA-55-8301 TCGA-55-8510 
        0.59        23.18        18.64        17.65         1.45        17.72 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-62-A46R TCGA-64-1679 TCGA-64-1681 
       16.93        22.65        20.58        56.71        55.43        38.37 
TCGA-64-5778 TCGA-67-6216 TCGA-69-8253 TCGA-69-8255 TCGA-73-4666 TCGA-73-7499 
       42.90         4.64        14.01         4.24        26.30        23.51 
TCGA-78-7143 TCGA-78-7153 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-86-6562 
      163.10        24.99       104.19        88.14        53.33        12.36 
TCGA-86-7711 TCGA-86-7954 TCGA-86-7955 TCGA-86-8076 TCGA-86-8671 TCGA-86-8672 
       34.39        19.89        16.70        16.08        27.58         0.62 
TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-7771 TCGA-93-7347 
       13.32        13.64        10.62         2.60        16.18         9.76 
TCGA-93-A4JP TCGA-95-8039 TCGA-95-A4VN TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 
       19.00        27.29        18.18         0.72         5.39        16.41 
TCGA-97-8547 TCGA-97-A4M3 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       21.60        17.75        49.35        37.35        86.04        58.85 
TCGA-MP-A4TC TCGA-NJ-A4YG TCGA-NJ-A4YI 
        2.43        62.60         0.13 

   0 HIGH  LOW 
0.07 0.00 0.13 
     0   HIGH    LOW 
223.96 214.62 163.10 
    0  HIGH   LOW 
17.77 17.29 19.00 
[1] "0.1 - 224.0 (17.8)" "0.0 - 214.6 (17.3)" "0.1 - 163.1 (19.0)"
D1V2, continuous
      vv
clus   STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  0          3       68       76        26        34         38          5
  HIGH       1       33       34        13        20         20          6
  LOW        0       22       23         7        13         12          0
      vv
clus   STAGE IV
  0          17
  HIGH        5
  LOW         3
D1V3, multiclass
            clus
vv            0 HIGH LOW
  STAGE I     3    1   0
  STAGE IA   68   33  22
  STAGE IB   76   34  23
  STAGE IIA  26   13   7
  STAGE IIB  34   20  13
  STAGE IIIA 38   20  12
  STAGE IIIB  5    6   0
  STAGE IV   17    5   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     84 149  24   9
  HIGH  42  68  13   9
  LOW   29  44   6   0
D1V4, multiclass
    clus
vv     0 HIGH LOW
  T1  84   42  29
  T2 149   68  44
  T3  24   13   6
  T4   9    9   0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus    N0  N1 N2+N3
  0    177  45    40
  HIGH  81  28    21
  LOW   49  16    11
D1V5, multiclass
       clus
vv        0 HIGH LOW
  N0    177   81  49
  N1     45   28  16
  N2+N3  40   21  11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus     0   1
  0    172  16
  HIGH  96   4
  LOW   59   3
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     172   16
  HIGH   96    4
  LOW    59    3
   clus
vv    0 HIGH LOW
  0 172   96  59
  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    145 123
  HIGH  70  62
  LOW   44  36
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     145  123
  HIGH   70   62
  LOW    44   36
        clus
vv         0 HIGH LOW
  FEMALE 145   70  44
  MALE   123   62  36
[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 ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  0                            13                                57
  HIGH                          3                                31
  LOW                           2                                14
      vv
clus   LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  0                                                   162
  HIGH                                                 80
  LOW                                                  52
      vv
clus   LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  0                                             4
  HIGH                                          0
  LOW                                           0
      vv
clus   LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  0                                               11
  HIGH                                             5
  LOW                                              3
      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                             9
  LOW                             0                             7
      vv
clus   LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  0                                                2
  HIGH                                             1
  LOW                                              2
      vv
clus   MUCINOUS (COLLOID) CARCINOMA
  0                               7
  HIGH                            2
  LOW                             0
D1V9, multiclass
                                                    clus
vv                                                     0 HIGH LOW
  LUNG ACINAR ADENOCARCINOMA                          13    3   2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                   57   31  14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 162   80  52
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS           4    0   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS       11    5   3
  LUNG CLEAR CELL ADENOCARCINOMA                       1    1   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                   3    0   0
  LUNG MUCINOUS ADENOCARCINOMA                         2    0   0
  LUNG PAPILLARY ADENOCARCINOMA                        6    9   7
  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"
D1V10, binary
      cls
clus     0   1
  0     12 256
  HIGH   5 127
  LOW    3  77
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      12  256
  HIGH    5  127
  LOW     3   77
     clus
vv      0 HIGH LOW
  NO   12    5   3
  YES 256  127  77
[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    168   7   1  17
  HIGH  87   4   2   4
  LOW   55   0   1   4
D1V13, multiclass
    clus
vv     0 HIGH LOW
  R0 168   87  55
  R1   7    4   0
  R2   1    2   1
  RX  17    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   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1     4                        21   206
  HIGH                                0     1                         6   106
  LOW                                 0     2                         2    65
D1V14, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   0
  ASIAN                              4    1   2
  BLACK OR AFRICAN AMERICAN         21    6   2
  WHITE                            206  106  65
[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      2 201
  HIGH   2  91
  LOW    2  57
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       2  201
  HIGH    2   91
  LOW     2   57
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       2    2   2
  NOT HISPANIC OR LATINO 201   91  57
[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    90  50
  FC.LOW.NONSIG 178  71
  FC.NEUTRAL     47  20
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          140           249            67 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           50            71            20 
$FC.HIGH.SIG
TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       19.96        45.01         0.00        24.03        47.05         8.02 
TCGA-05-4422 TCGA-05-4424 TCGA-05-5428 TCGA-05-5715 TCGA-38-4625 TCGA-38-4630 
       12.00        30.02        22.03         2.04        97.74        35.28 
TCGA-38-7271 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-6147 
       26.30        42.77        37.15        38.24         6.25        27.78 
TCGA-44-6777 TCGA-44-7661 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS 
       32.45        12.03        29.00        15.32        11.08        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4507 TCGA-49-4514 
       76.21        28.11        28.57        12.66         8.81        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5044 TCGA-50-5935 
       14.63        12.13        17.16        11.64        20.52        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-53-7624 
        8.45        15.12        22.55        42.35        25.55        34.29 
TCGA-55-5899 TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6979 TCGA-55-6982 
        2.86         0.79        42.51        48.49         7.79        32.71 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 
       70.26         0.20         3.12         1.28         1.12         0.53 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8205 TCGA-55-8208 TCGA-55-8511 
       29.72         3.29         5.06         1.08        22.16         0.30 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A493 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8399 
       16.93        20.71         0.92        20.19         4.57        88.64 
TCGA-62-A46O TCGA-62-A471 TCGA-64-1677 TCGA-64-1681 TCGA-67-3771 TCGA-67-6216 
       47.80        40.96        20.65        38.37        20.05         4.64 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-73-4658 TCGA-73-7499 
        5.42         2.30        12.56        14.01        52.60        23.51 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      163.10         5.69        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 
       19.50        32.09         5.88       104.19        88.14        26.53 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 
       53.33        10.75        10.55       214.62        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7954 TCGA-86-8056 TCGA-86-8076 
       12.36         5.88        34.39        19.89         4.57        16.08 
TCGA-86-8278 TCGA-86-8585 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4P7 TCGA-91-6830 
       15.65         1.15        27.58        13.32        13.64         1.97 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 
        2.60        12.23         7.36         1.18         9.76         6.12 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       19.00        17.29        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-97-7547 TCGA-97-7938 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
        2.76        64.60         0.59        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-8025 TCGA-J2-A4AD TCGA-MN-A4N4 
       21.44        17.75        20.84        34.85        18.08        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TK 
        2.76        86.14        37.35        58.85        14.10        19.13 
TCGA-NJ-A4YG TCGA-NJ-A4YP 
       62.60         1.64 

$FC.LOW.NONSIG
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       14.01        37.02         9.96        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96         9.01        29.98        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 
       25.02        24.00        15.02        15.02         9.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 
        5.98         8.68       120.79        37.71        49.05        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-5645 
       44.61        14.73         4.37        46.98        24.36        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       61.28        16.44        14.60        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       23.64        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       11.54        13.45        35.54        46.72        32.84        29.46 
TCGA-49-4512 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       29.75        29.26        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       31.04        49.28         9.27        14.27        40.60        78.67 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 
       29.03        25.12         3.91        11.05        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       10.13        25.61         7.59        13.94         9.21        48.62 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 
        0.07        32.65        40.73        15.25         0.82         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        5.49         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-7227 TCGA-55-7284 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
      107.21         1.74         7.99         0.13         1.32         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-7914 TCGA-55-8087 
        0.79         1.78         1.45         6.48         6.15        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
        1.51         2.17        15.42         0.76         0.36         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.49         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A492 TCGA-55-A494 
        1.58         1.61         2.17        21.40        19.59        15.81 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P 
       19.99        39.98        42.38        14.60        49.25        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3772 
       56.81        87.98         2.04        28.41        28.47        18.84 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04         5.72        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-71-6725 TCGA-71-8520 
       13.61         7.56         6.05        13.45         2.01         0.10 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        29.98        15.35         4.31         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 
        1.25        39.09        27.16        20.58        64.90        22.29 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 
        7.07       223.96         8.48        31.20         8.02        39.35 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
       32.68        39.75        77.59        31.13        13.87        20.55 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       19.43        24.49         4.08         0.79        15.75        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4P8 TCGA-91-6831 
       23.05        21.47        14.60        30.84        26.47        10.19 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       13.71        27.68         1.15        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7043 TCGA-95-7562 
       19.82         4.18        23.61         1.08         1.22         2.86 
TCGA-95-7567 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
       18.67        21.40        19.89        31.69        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
       25.48         5.95        18.67        17.92        18.12        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.58        20.19        19.76        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       36.76         1.45         5.59        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4SW 
       16.44        19.00         3.81         0.20        27.19        58.45 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A 
       11.05        14.66        73.91        71.05        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

$FC.NEUTRAL
TCGA-05-4249 TCGA-05-4250 TCGA-05-4427 TCGA-05-5423 TCGA-05-5425 TCGA-38-4629 
       50.07         3.98        26.01         4.96        29.00        28.41 
TCGA-44-2657 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       13.15        34.06        26.56        33.30        28.37        23.77 
TCGA-44-7660 TCGA-44-7662 TCGA-49-4505 TCGA-49-6767 TCGA-50-5072 TCGA-50-5941 
       19.46         7.17        14.07        22.26         8.22        18.64 
TCGA-50-6594 TCGA-50-6595 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-7281 
       12.16         6.21        27.25        30.54        23.05         0.59 
TCGA-55-7283 TCGA-55-7724 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
        1.15        23.18        18.64        17.65        19.82         0.16 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8510 TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 
        1.45         0.95        17.72        22.65         1.58        20.58 
TCGA-62-A46R TCGA-64-1679 TCGA-64-5778 TCGA-64-5781 TCGA-69-7979 TCGA-69-8255 
       56.71        55.43        42.90        51.25         2.93         4.24 
TCGA-69-A59K TCGA-73-4666 TCGA-78-7147 TCGA-78-7155 TCGA-78-8662 TCGA-86-7955 
        7.04        26.30        19.27        38.50       110.50        16.70 
TCGA-86-8073 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF 
       24.33        13.91         0.62        14.96        13.32        17.62 
TCGA-91-6828 TCGA-91-6829 TCGA-91-7771 TCGA-95-7039 TCGA-95-A4VN TCGA-97-7941 
       10.62        41.36        16.18         1.12        18.18         0.72 
TCGA-97-8174 TCGA-97-A4M2 TCGA-L4-A4E6 TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4TC 
        5.39        20.52        14.30        49.35        86.04         2.43 
TCGA-NJ-A4YI 
        0.13 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.00          0.07          0.13 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       214.62        223.96        110.50 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        18.54         17.92         18.18 
[1] "0.0 - 214.6 (18.5)" "0.1 - 224.0 (17.9)" "0.1 - 110.5 (18.2)"
D2V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  FC.HIGH.SIG         1       43       37        15        18         21
  FC.LOW.NONSIG       3       64       76        26        34         37
  FC.NEUTRAL          0       16       20         5        15         12
               vv
clus            STAGE IIIB STAGE IV
  FC.HIGH.SIG            6        7
  FC.LOW.NONSIG          5       17
  FC.NEUTRAL             0        1
D2V3, multiclass
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I              1             3          0
  STAGE IA            43            64         16
  STAGE IB            37            76         20
  STAGE IIA           15            26          5
  STAGE IIB           18            34         15
  STAGE IIIA          21            37         12
  STAGE IIIB           6             5          0
  STAGE IV             7            17          1
[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.SIG    55  75   8   9
  FC.LOW.NONSIG  79 149  24   9
  FC.NEUTRAL     21  37  11   0
D2V4, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1          55            79         21
  T2          75           149         37
  T3           8            24         11
  T4           9             9          0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1 N2+N3
  FC.HIGH.SIG    88  33    22
  FC.LOW.NONSIG 173  45    39
  FC.NEUTRAL     46  11    11
D2V5, multiclass
       clus
vv      FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0             88           173         46
  N1             33            45         11
  N2+N3          22            39         11
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
               cls
clus              0   1
  FC.HIGH.SIG   110   6
  FC.LOW.NONSIG 168  16
  FC.NEUTRAL     49   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    110    6
  FC.LOW.NONSIG  168   16
  FC.NEUTRAL      49    1
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0         110           168         49
  1           6            16          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    80  68
  FC.LOW.NONSIG 144 119
  FC.NEUTRAL     35  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     80   68
  FC.LOW.NONSIG  144  119
  FC.NEUTRAL      35   34
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          80           144         35
  MALE            68           119         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"
D2V8, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FC.HIGH.SIG                            3                                37
  FC.LOW.NONSIG                         13                                56
  FC.NEUTRAL                             2                                 9
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FC.HIGH.SIG                                                   88
  FC.LOW.NONSIG                                                160
  FC.NEUTRAL                                                    46
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  FC.HIGH.SIG                                            0
  FC.LOW.NONSIG                                          3
  FC.NEUTRAL                                             1
               vv
clus            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  FC.HIGH.SIG                                               3
  FC.LOW.NONSIG                                            11
  FC.NEUTRAL                                                5
               vv
clus            LUNG CLEAR CELL ADENOCARCINOMA
  FC.HIGH.SIG                                1
  FC.LOW.NONSIG                              1
  FC.NEUTRAL                                 0
               vv
clus            LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  FC.HIGH.SIG                                    0                            0
  FC.LOW.NONSIG                                  3                            2
  FC.NEUTRAL                                     0                            0
               vv
clus            LUNG PAPILLARY ADENOCARCINOMA
  FC.HIGH.SIG                              13
  FC.LOW.NONSIG                             5
  FC.NEUTRAL                                4
               vv
clus            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  FC.HIGH.SIG                                               1
  FC.LOW.NONSIG                                             2
  FC.NEUTRAL                                                2
               vv
clus            MUCINOUS (COLLOID) CARCINOMA
  FC.HIGH.SIG                              2
  FC.LOW.NONSIG                            7
  FC.NEUTRAL                               0
D2V9, multiclass
                                                    clus
vv                                                   FC.HIGH.SIG FC.LOW.NONSIG
  LUNG ACINAR ADENOCARCINOMA                                   3            13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           37            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          88           160
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                   0             3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                3            11
  LUNG CLEAR CELL ADENOCARCINOMA                               1             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                           0             3
  LUNG MUCINOUS ADENOCARCINOMA                                 0             2
  LUNG PAPILLARY ADENOCARCINOMA                               13             5
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                1             2
  MUCINOUS (COLLOID) CARCINOMA                                 2             7
                                                    clus
vv                                                   FC.NEUTRAL
  LUNG ACINAR ADENOCARCINOMA                                  2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)         46
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS               5
  LUNG CLEAR CELL ADENOCARCINOMA                              0
  LUNG MICROPAPILLARY ADENOCARCINOMA                          0
  LUNG MUCINOUS ADENOCARCINOMA                                0
  LUNG PAPILLARY ADENOCARCINOMA                               4
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA               2
  MUCINOUS (COLLOID) CARCINOMA                                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"
D2V10, binary
               cls
clus              0   1
  FC.HIGH.SIG     5 143
  FC.LOW.NONSIG  12 251
  FC.NEUTRAL      3  66
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      5  143
  FC.LOW.NONSIG   12  251
  FC.NEUTRAL       3   66
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO            5            12          3
  YES         143           251         66
[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    98   4   2   5
  FC.LOW.NONSIG 163   7   1  17
  FC.NEUTRAL     49   0   1   3
D2V13, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  R0          98           163         49
  R1           4             7          0
  R2           2             1          1
  RX           5            17          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"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.SIG                                  0     2
  FC.LOW.NONSIG                                1     4
  FC.NEUTRAL                                   0     1
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG                           5   119
  FC.LOW.NONSIG                        21   201
  FC.NEUTRAL                            3    57
D2V14, multiclass
                                  clus
vv                                 FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE           0             1          0
  ASIAN                                      2             4          1
  BLACK OR AFRICAN AMERICAN                  5            21          3
  WHITE                                    119           201         57
[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.SIG     3 100
  FC.LOW.NONSIG   2 196
  FC.NEUTRAL      1  53
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      3  100
  FC.LOW.NONSIG    2  196
  FC.NEUTRAL       1   53
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               3             2          1
  NOT HISPANIC OR LATINO         100           196         53
[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"
