[1] "ofn"        "-oTHNSC-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/HNSC-TP/22506490/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/HNSC-TP/22536208/APOBEC_clinical_corr_input_22541982/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=528, in cluster file=511, common to both=511
[1]   2 511
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 246  129  136 
   0 HIGH  LOW 
 246  129  136 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           224             41            246 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           224             41            246 
[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] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 511 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=203,	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=274,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=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=21,	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:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 511 columns, 1 survival variables, and 13 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"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  46 137  99 172 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   47   137    99   172 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  46 137  99 172 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   47   137    99   172 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
175  67 168   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
175  67 168   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
175  67 168   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
175  67 168   7 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=85, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=18, binary=FALSE, numeric=TRUE
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    151  93
  HIGH  75  54
  LOW   63  73
   0 HIGH  LOW 
 244  129  136 
   0 HIGH  LOW 
  93   54   73 
$`0`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6024 TCGA-CN-6992 
        9.30        68.48        30.18        51.29        11.08        35.05 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-A4C7 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-UF-A71D 
       24.39        48.20        11.61        40.24        21.11        48.03 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       15.19        13.64         9.07        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       23.84         4.01        41.85        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL 
        7.10         5.69         7.82         2.27        11.05        20.48 
TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
        6.15        18.38        66.28        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4733 TCGA-CN-4736 
        6.28        12.69        38.04         4.67        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 
       20.55        45.83        13.05        42.02        46.32        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6017 
       71.31         8.32        11.54        11.57        50.07        28.04 
TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C 
       34.13        10.45         3.68        35.01        23.57        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       31.69        22.32        12.07        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6222 
       52.37        21.50        70.45        62.37        10.42        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       53.52        77.56        29.49        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 
       16.90        11.34        12.46        22.78         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
       47.34        24.95         9.17        34.06        19.92        17.13 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7401 
       12.89        30.02        46.85        32.65         5.13        35.41 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
       29.95        17.16       129.21       108.95        76.24        17.95 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 
       94.88        91.53        23.05        86.83         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
       21.07        62.43         2.14         4.73        21.90        11.24 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       12.03        15.09        65.82         8.42        28.34         4.14 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       12.66         9.01        10.75       130.88         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 
       36.00        26.20        17.13        95.34        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7429 
        2.10        18.41        35.54         9.67        25.08         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A460 
       16.27        84.49         7.17       180.16       159.65        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
       67.86        56.61         7.07         5.98        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-D6-6515 
       28.01         3.62        21.24        23.47        19.92        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41         9.60        23.05        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        28.77         7.63        22.59        24.95 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W 
       18.02        37.58        37.18         3.02        18.94         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
       17.85        11.80        12.43        15.06        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 
       25.74        21.93        27.48         4.27         6.90        38.53 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       14.50        11.84        33.57         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       15.48        10.75         7.96        30.05         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       15.42         7.13        16.08        15.78        71.74        51.25 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       19.00        75.55        13.15        21.21        23.15        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        27.39        21.07        12.89         5.62        14.76 
TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        8.32         7.10        13.55        64.80        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       49.45        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66S TCGA-KU-A66T 
       22.36        17.03        13.35        18.15 

$HIGH
TCGA-BA-4077 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-A6V1 TCGA-CQ-6221 TCGA-CQ-7063 
       37.28         3.55        25.71        19.82        32.88        70.13 
TCGA-CR-6472 TCGA-CR-6478 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-5152 TCGA-BA-5558 
       34.52         6.02        22.85         2.96        42.35        65.59 
TCGA-BA-A6DJ TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4728 
       13.38       105.90         4.41        10.55        55.86        56.68 
TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5369 
       26.86        55.56        57.11        27.58        73.61        12.49 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-A49A TCGA-CN-A63Y TCGA-CQ-5326 
       56.94        30.67        23.90        17.29        16.57         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-7064 
       54.58        45.99        11.21         4.24        41.19        64.87 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-5248 TCGA-CR-6480 
       41.88        43.10        44.48        33.60        54.67        11.90 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 
       10.22        11.64        39.16        40.93         3.45         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7394 TCGA-CR-7395 
       29.23         0.99        47.01        27.06        44.25        30.58 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-6441 
       48.39       139.43        76.50        80.12        13.35         9.60 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6955 
        9.70         5.46        26.43       140.78        42.38        10.98 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7252 
        2.50        64.83        18.81         7.99         1.84         4.96 
TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45O 
       57.47         0.46       156.49        19.76        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A463 TCGA-CV-A6JE 
       21.01       169.38        35.47        45.96         0.76        35.34 
TCGA-CV-A6JM TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-A4ZB 
        6.38        22.52        10.42        10.55        18.84        12.36 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-F7-A50J TCGA-F7-A623 
       12.79        23.34        58.45        37.25        31.13        20.25 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-A61E 
       15.16        20.94        22.03         0.36        13.84        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       37.41         0.07        19.27        12.62        17.98        29.92 
TCGA-P3-A5QF TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A6II 
       10.85        18.97         2.04        29.00        12.99         9.34 
TCGA-QK-A6VC TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 
       19.73        15.32        12.72        16.96         6.87        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JA 
       13.71         3.12        13.25        20.35        44.65        74.47 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       20.75        32.65        20.55 

$LOW
TCGA-BA-5557 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6997 
       20.48        28.11         9.07         9.24        52.08        32.48 
TCGA-CQ-7068 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-HD-8634 
       43.04         0.36        34.36        30.94        14.04        12.66 
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
        3.35        26.50        15.52        21.17        14.83        12.62 
TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-8596 
       29.42        14.47        16.41         9.14         4.80        71.05 
TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-5358 TCGA-CN-5361 
       20.52        12.89        32.81        14.33         8.58        69.70 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6016 
       16.21        11.84         8.52        52.08        48.00        47.44 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
       19.07         6.74        32.22        38.89        17.42        11.74 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 
       25.41        29.72         7.40        12.39         4.41         2.70 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CR-5243 TCGA-CR-6473 
       15.75        32.38        23.24        29.36        84.23        36.99 
TCGA-CR-6474 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7382 
       18.54         7.69        15.75        35.84        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CV-5436 TCGA-CV-5440 
       32.78        49.58        24.79         5.95        19.20       107.51 
TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 
       17.92        48.59        60.49        54.74        90.12        20.52 
TCGA-CV-6943 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7090 
       19.79        30.08         6.08        53.95         7.13       172.67 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
      111.16         5.26        52.31        12.92        21.80        71.21 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7411 
       77.16        31.36        18.97        49.71       210.97        89.33 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 
       56.48       153.86        16.64         6.38        22.19        35.93 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A468 TCGA-CX-A4AQ 
        1.05         6.51        88.87        48.20        15.25        51.12 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5630 TCGA-DQ-7591 
        2.53        11.44        13.94        12.10        33.86        20.45 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 
       41.59        32.71        21.63        20.25        24.95        13.38 
TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-P3-A6SW 
       14.66         3.65        15.95        13.68        14.37        36.82 
TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-A8ZB 
       47.01        16.01        21.07         7.30        12.20        17.82 
TCGA-T2-A6WZ TCGA-UF-A71B TCGA-UF-A7JJ TCGA-WA-A7H4 
       15.91        49.51        18.05        14.56 

   0 HIGH  LOW 
0.46 0.07 0.07 
     0   HIGH    LOW 
180.16 169.38 210.97 
     0   HIGH    LOW 
20.715 22.030 20.520 
[1] "0.5 - 180.2 (20.7)" "0.1 - 169.4 (22.0)" "0.1 - 211.0 (20.5)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  0         14       42        41       115         6         1
  HIGH       4       16        12        73         2         0
  LOW        7       17        27        65         3         0
D1V3, multiclass
           clus
vv            0 HIGH LOW
  STAGE I    14    4   7
  STAGE II   42   16  17
  STAGE III  41   12  27
  STAGE IVA 115   73  65
  STAGE IVB   6    2   3
  STAGE IVC   1    0   0
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   T0+T1 T2 T3 T4
  0       27 71 46 78
  HIGH     8 27 19 56
  LOW     12 39 34 38
D1V4, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 27    8  12
  T2    71   27  39
  T3    46   19  34
  T4    78   56  38
[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    96 28 79  3
  HIGH 43 15 42  1
  LOW  36 24 47  3
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 96   43  36
  N1 28   15  24
  N2 79   42  47
  N3  3    1   3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus    0  1
  0    99  1
  HIGH 50  0
  LOW  42  0
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      99    1
  HIGH   50    0
  LOW    42    0
   clus
vv   0 HIGH LOW
  0 99   50  42
  1  1    0   0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
      cls
clus     0   1
  0     54 192
  HIGH  49  80
  LOW   35 101
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      54  192
  HIGH   49   80
  LOW    35  101
        clus
vv         0 HIGH LOW
  FEMALE  54   49  35
  MALE   192   80 101
[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     74 145
  HIGH  46  74
  LOW   37  74
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      74  145
  HIGH   46   74
  LOW    37   74
     clus
vv      0 HIGH LOW
  NO   74   46  37
  YES 145   74  74
[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"
      vv
clus   HEAD & NECK SQUAMOUS CELL CARCINOMA
  0                                    239
  HIGH                                 126
  LOW                                  135
      vv
clus   HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  0                                                    6
  HIGH                                                 3
  LOW                                                  1
      vv
clus   HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  0                                                            1
  HIGH                                                         0
  LOW                                                          0
D1V9, multiclass
                                                           clus
vv                                                            0 HIGH LOW
  HEAD & NECK SQUAMOUS CELL CARCINOMA                       239  126 135
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE           6    3   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT   1    0   0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
D1V12, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1     5                        28   205
  HIGH                                0     4                         9   115
  LOW                                 1     1                        10   117
D1V13, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   1
  ASIAN                              5    4   1
  BLACK OR AFRICAN AMERICAN         28    9  10
  WHITE                            205  115 117
[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"
D1V14, binary
      cls
clus     0   1
  0     11 212
  HIGH   7 113
  LOW    7 124
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      11  212
  HIGH    7  113
  LOW     7  124
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      11    7   7
  NOT HISPANIC OR LATINO 212  113 124
[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"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH 122 102
  FC.LOW.ENRICH   16  25
  FC.NO.ENRICH   151  93
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           224             41            244 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           102             25             93 
$FC.HIGH.ENRICH
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6022 
       37.28        20.48         3.55        28.11        25.71         9.24 
TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       52.08        32.48        19.82        32.88        70.13        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-HD-8634 
       34.52         6.02         0.36        34.36        14.04        12.66 
TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5558 
       22.85         2.96         3.35        26.50        42.35        65.59 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DJ 
       15.52        14.83        12.62        29.42        14.47        13.38 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-A5HY 
       16.41       105.90         9.14         4.41        71.05        10.55 
TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4734 
       55.86        56.68        12.89        26.86        32.81        55.56 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5361 
       57.11        14.33        27.58        73.61         8.58        69.70 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
       16.21        11.84        12.49         8.52        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       48.00        23.90        47.44         6.74        32.22        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63Y 
       17.42        11.74        25.41        17.29        29.72        16.57 
TCGA-CN-A640 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        4.41         2.93        54.58        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7071 
       41.19        15.75        32.38        64.87        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-6473 
       44.48        23.24        33.60        84.23        54.67        36.99 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
       18.54        11.90        10.22        11.64         7.69        15.75 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       39.16        40.93        35.84         3.09        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7394 
       31.96        32.78        47.01        27.06        49.58        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5440 
       30.58        24.79        48.39       139.43        19.20       107.51 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
       76.50        80.12        17.92        13.35        48.59        60.49 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 
       54.74         9.60        90.12         9.70         5.46        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 
      140.78        19.79        42.38        30.08         6.08        10.98 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7103 
        2.50        64.83        18.81         7.99         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7261 
       12.92        21.80        77.16        18.97         4.96        49.71 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7423 
       57.47       210.97         0.46        22.85         0.07       100.57 
TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-A45O 
      156.49        19.76       153.86         6.38        35.93        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 
       21.01       169.38        35.47         1.05        88.87         0.76 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       35.34         6.38        10.42        10.55        18.84        51.12 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        2.53        11.44        12.36        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7596 
       23.34        58.45        37.25        33.86        20.45        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A623 
       32.71        21.63        20.25        31.13        24.95        20.25 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       15.16        20.94        22.03         0.36        13.84         3.65 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A51W 
       37.71        37.41         0.07        13.68        19.27        14.37 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T3 
       12.62        17.98        29.92        10.85        36.82        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG 
        2.04        29.00        12.99        16.01        21.07         7.30 
TCGA-QK-A6II TCGA-QK-A6VC TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO 
        9.34        19.73        12.20        17.82        15.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ 
       16.96         6.87        32.45        13.71         3.12        13.25 
TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT 
       20.35        44.65        74.47        18.05        20.75        32.65 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

$FC.LOW.ENRICH
TCGA-CN-6021 TCGA-DQ-5629 TCGA-BA-6869 TCGA-BB-4225 TCGA-BB-8601 TCGA-CN-5373 
        9.07        30.94        21.17         4.80        20.52        52.08 
TCGA-CN-6018 TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A642 TCGA-CQ-A4CB TCGA-CR-7370 
       19.07         7.40        12.39         2.70        29.36         3.45 
TCGA-CR-7382 TCGA-CR-7399 TCGA-CV-6937 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7090 
       26.17         5.95        20.52        53.95         7.13       172.67 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7243 TCGA-CV-7411 TCGA-CV-7418 
      111.16         5.26        71.21        31.36        89.33        25.94 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7568 
       34.09        14.89        56.48        16.64        22.19        30.48 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6K1 TCGA-H7-7774 
       45.96         6.51        48.20        15.25        22.52        13.38 
TCGA-HD-8224 TCGA-IQ-7630 TCGA-P3-A6SX TCGA-T2-A6WZ TCGA-UF-A71B 
       14.66        15.95        47.01        15.91        49.51 

$FC.NO.ENRICH
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6024 TCGA-CN-6992 
        9.30        68.48        30.18        51.29        11.08        35.05 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-A4C7 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-UF-A71D 
       24.39        48.20        11.61        40.24        21.11        48.03 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       15.19        13.64         9.07        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       23.84         4.01        41.85        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL 
        7.10         5.69         7.82         2.27        11.05        20.48 
TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
        6.15        18.38        66.28        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4733 TCGA-CN-4736 
        6.28        12.69        38.04         4.67        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 
       20.55        45.83        13.05        42.02        46.32        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6017 
       71.31         8.32        11.54        11.57        50.07        28.04 
TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C 
       34.13        10.45         3.68        35.01        23.57        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       31.69        22.32        12.07        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6222 
       52.37        21.50        70.45        62.37        10.42        66.28 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       53.52        77.56        29.49        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 
       16.90        11.34        12.46        22.78         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
       47.34        24.95         9.17        34.06        19.92        17.13 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7401 
       12.89        30.02        46.85        32.65         5.13        35.41 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
       29.95        17.16       129.21       108.95        76.24        17.95 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 
       94.88        91.53        23.05        86.83         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
       21.07        62.43         2.14         4.73        21.90        11.24 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       12.03        15.09        65.82         8.42        28.34         4.14 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       12.66         9.01        10.75       130.88         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 
       36.00        26.20        17.13        95.34        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7429 
        2.10        18.41        35.54         9.67        25.08         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A460 
       16.27        84.49         7.17       180.16       159.65        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
       67.86        56.61         7.07         5.98        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-D6-6515 
       28.01         3.62        21.24        23.47        19.92        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41         9.60        23.05        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        28.77         7.63        22.59        24.95 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W 
       18.02        37.58        37.18         3.02        18.94         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
       17.85        11.80        12.43        15.06        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 
       25.74        21.93        27.48         4.27         6.90        38.53 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG 
       14.50        11.84        33.57         5.29        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       15.48        10.75         7.96        30.05         1.84         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       15.42         7.13        16.08        15.78        71.74        51.25 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       19.00        75.55        13.15        21.21        23.15        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        27.39        21.07        12.89         5.62        14.76 
TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        8.32         7.10        13.55        64.80        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       49.45        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66S TCGA-KU-A66T 
       22.36        17.03        13.35        18.15 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.07           2.70           0.46 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        210.97         172.67         180.16 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        20.975         21.170         20.715 
[1] "0.1 - 211.0 (21.0)" "2.7 - 172.7 (21.2)" "0.5 - 180.2 (20.7)"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  FC.HIGH.ENRICH       9       25        31       121         4         0
  FC.LOW.ENRICH        2        8         8        17         1         0
  FC.NO.ENRICH        14       42        41       115         6         1
D2V3, multiclass
           clus
vv          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                9             2           14
  STAGE II              25             8           42
  STAGE III             31             8           41
  STAGE IVA            121            17          115
  STAGE IVB              4             1            6
  STAGE IVC              0             0            1
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  FC.HIGH.ENRICH    16 55 43 82
  FC.LOW.ENRICH      4 11 10 12
  FC.NO.ENRICH      27 71 46 78
D2V4, multiclass
       clus
vv      FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T0+T1             16             4           27
  T2                55            11           71
  T3                43            10           46
  T4                82            12           78
[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 67 33 77  3
  FC.LOW.ENRICH  12  6 12  1
  FC.NO.ENRICH   96 28 79  3
D2V5, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0             67            12           96
  N1             33             6           28
  N2             77            12           79
  N3              3             1            3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus              0  1
  FC.HIGH.ENRICH 80  0
  FC.LOW.ENRICH  12  0
  FC.NO.ENRICH   99  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   80    0
  FC.LOW.ENRICH    12    0
  FC.NO.ENRICH     99    1
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0             80            12           99
  1              0             0            1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  71 153
  FC.LOW.ENRICH   13  28
  FC.NO.ENRICH    54 192
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   71  153
  FC.LOW.ENRICH    13   28
  FC.NO.ENRICH     54  192
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE             71            13           54
  MALE              153            28          192
[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  76 126
  FC.LOW.ENRICH    7  22
  FC.NO.ENRICH    74 145
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   76  126
  FC.LOW.ENRICH     7   22
  FC.NO.ENRICH     74  145
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO              76             7           74
  YES            126            22          145
[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"
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA
  FC.HIGH.ENRICH                                 220
  FC.LOW.ENRICH                                   41
  FC.NO.ENRICH                                   239
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FC.HIGH.ENRICH                                                 4
  FC.LOW.ENRICH                                                  0
  FC.NO.ENRICH                                                   6
                vv
clus             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  FC.HIGH.ENRICH                                                         0
  FC.LOW.ENRICH                                                          0
  FC.NO.ENRICH                                                           1
D2V9, multiclass
                                                           clus
vv                                                          FC.HIGH.ENRICH
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  220
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                      4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT              0
                                                           clus
vv                                                          FC.LOW.ENRICH
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                  41
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT             0
                                                           clus
vv                                                          FC.NO.ENRICH
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                239
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                    6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT            1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
D2V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.ENRICH                                1     4
  FC.LOW.ENRICH                                 0     1
  FC.NO.ENRICH                                  1     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH                        17   197
  FC.LOW.ENRICH                          2    35
  FC.NO.ENRICH                          28   205
D2V13, multiclass
                                  clus
vv                                 FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE              1             0            1
  ASIAN                                         4             1            5
  BLACK OR AFRICAN AMERICAN                    17             2           28
  WHITE                                       197            35          205
[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"
D2V14, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  11 202
  FC.LOW.ENRICH    3  35
  FC.NO.ENRICH    11 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   11  202
  FC.LOW.ENRICH     3   35
  FC.NO.ENRICH     11  212
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                 11             3           11
  NOT HISPANIC OR LATINO            202            35          212
[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"
