[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/19775211/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/HNSC-TP/20203263/APOBEC_clinical_corr_input_20214860/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=528, in cluster file=510, common to both=510
[1]   2 510
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 251  129  130 
   0 HIGH  LOW 
 251  129  130 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          219           250            41 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          219           250            41 
[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 510 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=200,	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=325,	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=5,	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=2,	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=22,	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=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	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 510 columns, 1 survival variables, and 12 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] "GENDER"                        "RADIATION_THERAPY"            
 [7] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "NUMBER_OF_LYMPH_NODES"        
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=5, 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  47 134  99 168 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   48   134    99   168 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  47 134  99 168 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   48   134    99   168 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
175  67 162   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
175  67 162   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
175  67 162   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
175  67 162   7 
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=86, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=58, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=19, 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    157  94
  HIGH  76  53
  LOW   60  70
   0 HIGH  LOW 
 251  129  130 
   0 HIGH  LOW 
  94   53   70 
$`0`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 
       15.19         9.30        13.64         9.07        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       17.10        23.84        68.48         4.01        41.85        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       30.18        27.95        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7861 
        2.27        11.05        20.48         6.15        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UM 
       36.72        33.70        50.20        66.28        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        8.81         6.28        12.69        38.04         4.67        51.29 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       52.14        12.99        20.55        45.83        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
       46.32        12.39        71.31         8.32        11.54        11.57 
TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
       50.07        28.04        34.13        11.08        10.45        35.05 
TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
        3.68        35.01        23.57        21.21        31.69        22.32 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       12.07        23.44        24.39        20.88        19.53        48.20 
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-7067 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG 
       53.52        16.73        77.56        11.61        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       12.46        31.23        11.77        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6488 TCGA-CR-6491 
       50.01        39.52        16.90        11.34        12.46        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 
        9.27        47.18        47.34        24.95         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       19.92        17.13        12.89        30.02        46.85        32.65 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        5.13        35.41        29.95        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 
       76.24        17.95        87.55        91.53        23.05        86.83 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6938 
        7.07        43.23        21.07        62.43         2.14         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6959 
       21.90        11.24        12.03        15.09        65.82         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 
       28.34         4.14        12.66         9.01        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        4.73        47.47        36.00        26.20        17.13        95.34 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       11.87        47.97         2.10        18.41        35.54        17.85 
TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        9.67        25.08         3.52        16.27        84.49         7.17 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
      180.16       159.65        60.43        67.86        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       15.25         5.98        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       21.24        23.47        19.92        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       23.05        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-DQ-5631 TCGA-DQ-7589 
       28.77         7.63        22.59        24.95        18.02        46.32 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I 
       46.45        37.58        40.24        39.12        37.18         3.02 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-A6C4 
       18.94         0.46        17.85        11.80        12.43        13.61 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       21.11         0.07        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
       27.48         4.27         6.90        38.53        14.50        11.84 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S 
       33.57         5.29        13.84        19.04        15.48        13.35 
TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       18.15        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-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 
       12.72        18.64        21.07         7.10        13.55        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD 
       54.67         2.83        48.03        49.45        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       55.43        29.46        13.94        22.36        17.03 

$HIGH
TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-A6DJ TCGA-BB-4223 
       37.28        42.35        65.59         3.55        13.38       105.90 
TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4728 
        4.41        24.66        25.71        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-CN-A6V1 
       56.94        30.67        23.90        17.29        16.57        19.82 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        2.93        54.58        45.99        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       32.88        70.13        64.87        41.88        43.10        44.48 
TCGA-CQ-A4CD TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       33.60        54.67        34.52         6.02        11.90        10.22 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       11.64        39.16        40.93         3.45         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7404 
        0.99        47.01        27.06        44.25        30.58        48.39 
TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-6441 
      139.43       107.51        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-DQ-7594 TCGA-F7-A50J 
       12.79        11.11        58.45        37.25        40.04        31.13 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
       20.25        15.16        20.94        22.03        22.85         0.36 
TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-KU-A6H7 
       13.84        34.75        37.71        37.41         0.07        19.27 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5QF TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       12.62        17.98        10.85        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-QK-A6II TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.99         9.34        19.73        12.72        16.96         6.87 
TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JO 
       32.45        13.25        20.35        44.65        74.47        20.75 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ 
       32.65         2.96        20.55 

$LOW
TCGA-BA-5149 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       26.50        20.48        15.52        21.17        14.83        12.62 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7872 
       29.42        28.11        14.47         9.14         4.60        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-5358 
       71.05        20.52        12.89        32.81        14.33         8.58 
TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
       69.70        16.21        11.84         8.52        52.08        48.00 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       47.44        19.07         6.74         9.07         9.24        52.08 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
       32.22        38.89        17.42        32.48        11.74        25.41 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-6219 
       29.72         7.40        12.39         4.41         2.70        15.75 
TCGA-CQ-6220 TCGA-CQ-7068 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CR-5243 TCGA-CR-6473 
       32.38        43.04        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-5966 
       32.78        29.82         7.10         5.95        19.20        17.92 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6943 
       48.59        60.49        54.74        90.12        20.52        19.79 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7090 TCGA-CV-7091 
       30.08         6.08        53.95         7.13       126.15       111.16 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 
        5.26        52.31        12.92        21.80        71.21        77.16 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 
       31.36        18.97        36.13       210.97        89.33        22.85 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45V 
      153.86        16.64         6.38        22.19        35.93         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CX-7082 TCGA-CX-7219 TCGA-CX-A4AQ 
        6.51        88.87        48.20        10.42        34.36        51.12 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-5630 
        2.53        11.44        13.94        12.10        30.94        33.86 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V 
       14.04        20.45        41.59        21.63        20.25        24.95 
TCGA-H7-7774 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61L 
       13.38        14.66        12.66         3.65        15.95        13.68 
TCGA-MT-A51W TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG 
       14.37        36.82        47.01        16.01        21.07         7.30 
TCGA-T2-A6WZ TCGA-UF-A71B TCGA-UF-A7JJ TCGA-WA-A7H4 
       15.91        49.51        18.05        14.56 

   0 HIGH  LOW 
0.07 0.07 0.07 
     0   HIGH    LOW 
180.16 169.38 210.97 
     0   HIGH    LOW 
21.070 22.850 20.795 
[1] "0.1 - 180.2 (21.1)" "0.1 - 169.4 (22.9)" "0.1 - 211.0 (20.8)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  0         15       42        43       115         7
  HIGH       3       16        12        72         2
  LOW        7       17        27        61         2
D1V3, multiclass
           clus
vv            0 HIGH LOW
  STAGE I    15    3   7
  STAGE II   42   16  17
  STAGE III  43   12  27
  STAGE IVA 115   72  61
  STAGE IVB   7    2   2
[1] 5 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       29 72 46 77
  HIGH     7 25 19 57
  LOW     12 37 34 34
D1V4, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 29    7  12
  T2    72   25  37
  T3    46   19  34
  T4    77   57  34
[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    98 28 78  4
  HIGH 42 15 41  1
  LOW  35 24 43  2
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 98   42  35
  N1 28   15  24
  N2 78   41  43
  N3  4    1   2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
      cls
clus     0   1
  0     55 196
  HIGH  50  79
  LOW   35  95
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      55  196
  HIGH   50   79
  LOW    35   95
        clus
vv         0 HIGH LOW
  FEMALE  55   50  35
  MALE   196   79  95
[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     71 138
  HIGH  41  73
  LOW   34  63
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      71  138
  HIGH   41   73
  LOW    34   63
     clus
vv      0 HIGH LOW
  NO   71   41  34
  YES 138   73  63
[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 AND NECK SQUAMOUS CELL CARCINOMA
  0                                      245
  HIGH                                   128
  LOW                                    129
      vv
clus   HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  0                                                              1
  HIGH                                                           0
  LOW                                                            0
      vv
clus   HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  0                                                      5
  HIGH                                                   1
  LOW                                                    1
D1V8, multiclass
                                                             clus
vv                                                              0 HIGH LOW
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                       245  128 129
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT   1    0   0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE           5    1   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"
D1V9, continuous
D1V10, continuous
D1V11, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1     5                        25   213
  HIGH                                0     4                         6   118
  LOW                                 1     2                         6   115
D1V12, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   1
  ASIAN                              5    4   2
  BLACK OR AFRICAN AMERICAN         25    6   6
  WHITE                            213  118 115
[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"
D1V13, binary
      cls
clus     0   1
  0     13 216
  HIGH   7 113
  LOW    6 119
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      13  216
  HIGH    7  113
  LOW     6  119
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      13    7   6
  NOT HISPANIC OR LATINO 216  113 119
[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   120  99
  FC.LOW.NONSIG 156  94
  FC.NEUTRAL     17  24
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          219           250            41 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           99            94            24 
$FC.HIGH.SIG
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       37.28        26.50        42.35        20.48        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DE 
       14.83         3.55        12.62        29.42        28.11        14.47 
TCGA-BA-A6DJ TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-7872 
       13.38       105.90         9.14         4.41        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4728 
       71.05        20.52        25.71        10.55        55.86        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4738 
       12.89        26.86        32.81        55.56        57.11        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5366 
       27.58        73.61         8.58        69.70        16.21        11.84 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       12.49         8.52        56.94        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 
       47.44         6.74         9.24        52.08        32.22        38.89 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        32.48        11.74        25.41        17.29        29.72 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A6V1 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 
       16.57         4.41        19.82         2.93        54.58        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6221 
       11.21         4.24        41.19        15.75        32.38        32.88 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        64.87        43.04        41.88        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       23.24        33.60        54.67        34.52        36.99        18.54 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
        6.02        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        29.82        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5440 
       30.58         7.10        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        36.13 
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-7082 TCGA-CX-7085 TCGA-CX-7086 
       35.34         6.38        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-CX-A4AQ TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP 
       34.36        51.12         2.53        11.44        12.36        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        37.25        33.86 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G 
       14.04        20.45        40.04        41.59        21.63        20.25 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-8314 
       31.13        24.95        20.25        15.16        20.94        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 
       12.66        22.85         0.36        13.84         3.65        34.75 
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-A5QF TCGA-P3-A6SW TCGA-P3-A6T3 TCGA-P3-A6T4 
       12.62        17.98        10.85        36.82        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6II 
       29.00        12.99        16.01        21.07         7.30         9.34 
TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HJ 
       19.73        12.72        16.96         6.87        32.45        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-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        20.55        14.56 

$FC.LOW.NONSIG
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 
       15.19         9.30        13.64         9.07        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       17.10        23.84        68.48         4.01        41.85        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       30.18        27.95        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7861 
        2.27        11.05        20.48         6.15        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UM 
       36.72        33.70        50.20        66.28        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        8.81         6.28        12.69        38.04         4.67        51.29 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       52.14        12.99        20.55        45.83        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
       46.32        12.39        71.31         8.32        11.54        11.57 
TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
       50.07        28.04        34.13        11.08        10.45        35.05 
TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
        3.68        35.01        23.57        21.21        31.69        22.32 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       12.07        23.44        24.39        20.88        19.53        48.20 
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-7067 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG 
       53.52        16.73        77.56        11.61        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       12.46        31.23        11.77        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6488 TCGA-CR-6491 
       50.01        39.52        16.90        11.34        12.46        22.78 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 
        9.27        47.18        47.34        24.95         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7398 
       19.92        17.13        12.89        46.85        32.65         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        29.95        17.16       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 
       17.95        87.55        91.53        23.05        86.83         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6939 
       43.23        21.07        62.43         2.14         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 
       11.24        12.03        15.09        65.82         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
        4.14        12.66         9.01        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 
       47.47        36.00        26.20        17.13        95.34        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 
       47.97         2.10        18.41        35.54        17.85         9.67 
TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45R 
       25.08         3.52        16.27        84.49         7.17       180.16 
TCGA-CV-A45T TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
      159.65        60.43        67.86        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        5.98        29.79         6.48        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       23.47        19.92        13.25        25.41         9.60        23.05 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
       16.14        18.67        24.95        25.32        17.72        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
        7.63        22.59        24.95        18.02        46.32        46.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61S 
       37.58        40.24        39.12        37.18         3.02        18.94 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-A6C4 TCGA-H7-A6C5 
        0.46        17.85        11.80        12.43        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
        0.07        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J 
        4.27         6.90        38.53        14.50        11.84        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A66S TCGA-KU-A66T 
        5.29        13.84        19.04        15.48        13.35        18.15 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN 
       10.75         7.96        30.05         1.84         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 
        7.13        16.08        15.78        71.74        51.25        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ 
       75.55        13.15        21.21        23.15        21.47        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A719 
       18.64        21.07         7.10        13.55        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        2.83        48.03        49.45        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       29.46        13.94        22.36        17.03 

$FC.NEUTRAL
TCGA-BA-6869 TCGA-BB-4225 TCGA-CN-5373 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-A63T 
       21.17         4.60        52.08        19.07         9.07         7.40 
TCGA-CN-A63W TCGA-CN-A642 TCGA-CQ-A4CB TCGA-CR-5243 TCGA-CR-7370 TCGA-CR-7382 
       12.39         2.70        29.36        84.23         3.45        26.17 
TCGA-CR-7391 TCGA-CR-7399 TCGA-CV-6937 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7090 
       30.02         5.95        20.52        53.95         7.13       126.15 
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-A6K1 TCGA-DQ-5629 TCGA-H7-7774 
       45.96         6.51        48.20        22.52        30.94        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.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.07          0.07          2.70 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       210.97        180.16        126.15 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        21.07         21.07         22.52 
[1] "0.1 - 211.0 (21.1)" "0.1 - 180.2 (21.1)" "2.7 - 126.2 (22.5)"
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FC.HIGH.SIG         8       25        32       117         3
  FC.LOW.NONSIG      14       42        43       115         7
  FC.NEUTRAL          3        8         7        16         1
D2V3, multiclass
           clus
vv          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I             8            14          3
  STAGE II           25            42          8
  STAGE III          32            43          7
  STAGE IVA         117           115         16
  STAGE IVB           3             7          1
[1] 5 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.SIG      15 51 44 80
  FC.LOW.NONSIG    28 72 46 77
  FC.NEUTRAL        5 11  9 11
D2V4, multiclass
       clus
vv      FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T0+T1          15            28          5
  T2             51            72         11
  T3             44            46          9
  T4             80            77         11
[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   65 34 73  2
  FC.LOW.NONSIG 97 28 78  4
  FC.NEUTRAL    13  5 11  1
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0          65            97         13
  N1          34            28          5
  N2          73            78         11
  N3           2             4          1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
               cls
clus              0   1
  FC.HIGH.SIG    72 147
  FC.LOW.NONSIG  54 196
  FC.NEUTRAL     14  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     72  147
  FC.LOW.NONSIG   54  196
  FC.NEUTRAL      14   27
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          72            54         14
  MALE           147           196         27
[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    69 116
  FC.LOW.NONSIG  70 138
  FC.NEUTRAL      7  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     69  116
  FC.LOW.NONSIG   70  138
  FC.NEUTRAL       7   20
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO           69            70          7
  YES         116           138         20
[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 AND NECK SQUAMOUS CELL CARCINOMA
  FC.HIGH.SIG                                     217
  FC.LOW.NONSIG                                   244
  FC.NEUTRAL                                       41
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  FC.HIGH.SIG                                                             0
  FC.LOW.NONSIG                                                           1
  FC.NEUTRAL                                                              0
               vv
clus            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  FC.HIGH.SIG                                                     2
  FC.LOW.NONSIG                                                   5
  FC.NEUTRAL                                                      0
D2V8, multiclass
                                                             clus
vv                                                            FC.HIGH.SIG
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                               217
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                   2
                                                             clus
vv                                                            FC.LOW.NONSIG
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                 244
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                     5
                                                             clus
vv                                                            FC.NEUTRAL
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                               41
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                  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"
D2V9, continuous
D2V10, continuous
D2V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.SIG                                  1     5
  FC.LOW.NONSIG                                1     5
  FC.NEUTRAL                                   0     1
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG                          11   197
  FC.LOW.NONSIG                        25   212
  FC.NEUTRAL                            1    37
D2V12, multiclass
                                  clus
vv                                 FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE           1             1          0
  ASIAN                                      5             5          1
  BLACK OR AFRICAN AMERICAN                 11            25          1
  WHITE                                    197           212         37
[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"
D2V13, binary
               cls
clus              0   1
  FC.HIGH.SIG    11 197
  FC.LOW.NONSIG  13 215
  FC.NEUTRAL      2  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     11  197
  FC.LOW.NONSIG   13  215
  FC.NEUTRAL       2   36
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO              11            13          2
  NOT HISPANIC OR LATINO         197           215         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"
