[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/15078978/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/HNSC-TP/15648694/APOBEC_clinical_corr_input_15648744/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=522, in cluster file=510, common to both=506
[1]   2 506
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 252  127  127 
   0 HIGH  LOW 
 252  127  127 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          220           251            35 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          220           251            35 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 506 columns.

[1] "Batch" "22"   
[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=186,	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=322,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 506 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "GENDER"                                
 [6] "HISTOLOGICAL_TYPE"                     
 [7] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [8] "NUMBER_PACK_YEARS_SMOKED"              
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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  47 131  98 168 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   48   131    98   168 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  47 131  98 168 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   48   131    98   168 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
174  65 161   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
174  65 161   7 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
174  65 161   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
174  65 161   7 
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, 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=23, 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    163  87
  HIGH  77  50
  LOW   63  64
   0 HIGH  LOW 
 250  127  127 
   0 HIGH  LOW 
  87   50   64 
$`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        57.44         4.01         7.76        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-4225 TCGA-BB-4228 
        2.27        11.05        20.48         6.15         4.60        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ 
       22.42        36.72        33.70        50.20        66.28        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 
       40.44        21.11        12.99        20.55        43.73        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
       33.11        34.36        12.39        35.54         8.32        11.54 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 
       11.57        20.71        20.68        14.20        11.08        10.45 
TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T 
       12.95         3.68        35.01        17.59        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 
       17.29        15.91        12.07        10.09         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
        6.18        48.20        39.68        21.50        46.75        45.80 
TCGA-CQ-5332 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       10.42        66.28        34.75        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE 
       14.99        38.76        33.11        64.11        11.61        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        11.77        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6477 TCGA-CR-6482 
       26.27        58.42        50.01        39.52        16.90        11.34 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7372 
       12.46        11.51         9.27        47.18        47.34        24.95 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7391 
        9.17        34.06        19.92        17.13        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 
       31.10        29.85         5.13        35.41        29.95        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 
      129.21       108.95        76.24        17.95        94.88        91.53 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       23.05        86.83         7.07        43.23        21.07        62.43 
TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
        2.14         4.73        21.90        11.24        12.03        15.09 
TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 
       65.82         8.42        28.34         4.14       126.15        12.66 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 
        9.01        10.75       130.88         4.73        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       26.20        17.13        95.34        11.87        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7429 
       18.41        35.54        17.85         9.67        25.08         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45T 
       16.27        84.49         7.17        22.19       180.16       159.65 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JN 
       60.43        67.86        56.61         7.07         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6827 
       13.25        25.41         9.60        23.05        16.14        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        25.32        17.72        15.88         7.63        14.30 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
       10.65        37.18         3.02        18.94         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       11.80        12.43        13.61        21.11         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
       25.74         1.22         4.27         6.90        12.76        14.50 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       11.84        14.47         5.29        11.84        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         3.68        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        56.75        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        11.74        17.65        16.70        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A719 
       18.64        14.79         7.10        13.55        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        2.83        41.16        42.02        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       21.86        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        53.79         3.55        13.38        94.62 
TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4730 
        4.41        24.66        25.71        10.55        23.70        26.86 
TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5369 TCGA-CN-5374 
       24.92        41.10        27.58        41.69        12.49        56.94 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-A49A TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5326 
       30.67        20.65        12.85         5.75         7.33         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       54.58        45.99        11.21         4.24        41.19        32.88 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD 
       70.13        51.29        41.88        28.83        44.48        32.81 
TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
       54.67        34.52         6.02        11.90        10.22        11.64 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       39.16        40.93         3.45         3.09        29.23         0.99 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5430 
       47.01        27.06        29.52        30.58        48.39       139.43 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-6441 TCGA-CV-6935 
      107.51        76.50        80.12        13.35         9.60         9.70 
TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6955 TCGA-CV-6961 
        5.46        26.43       126.08        42.38        10.98         2.50 
TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7252 TCGA-CV-7406 
       64.83        18.81         7.99         1.84         4.96        57.47 
TCGA-CV-7414 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45O 
        0.46        14.89       156.49        19.76        30.48        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A463 TCGA-CV-A6JE TCGA-CV-A6JM 
       24.99       169.38        35.47         0.76        35.34         6.38 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-A4ZB TCGA-D6-A6ES 
       22.52        10.42        10.55        18.84        12.36        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7594 TCGA-F7-A50J TCGA-F7-A623 TCGA-H7-8501 
       11.11        35.54        12.10        19.23        20.25        15.16 
TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 
        6.77        22.03        22.85         0.36        13.84        34.75 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67F TCGA-MZ-A7D7 
       19.33        13.55         0.07        12.43        12.62        17.98 
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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HJ 
       12.43        12.72        16.96         6.87        32.45        13.25 
TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV 
       13.68        44.65        62.27        20.75        32.65         2.96 
TCGA-WA-A7GZ 
       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-7872 TCGA-BB-8596 
       29.42        28.11        14.47         9.14        38.40        71.05 
TCGA-BB-8601 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-5358 
       20.52        37.84        12.89        32.65        14.33         8.58 
TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
       55.27        16.21        11.84         8.52        22.45        20.68 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.53        19.07         6.74         9.07         9.24        36.49 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
       20.09        24.16        17.42        14.10        11.74        14.56 
TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-6219 TCGA-CQ-6220 
       29.72        11.44         4.41         2.70        15.75        32.38 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CR-6473 TCGA-CR-6474 
       16.73        43.04        23.24        29.36        36.99        18.54 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 
        7.69        15.75        35.84        31.96        26.17        32.78 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CV-5436 TCGA-CV-5966 TCGA-CV-5976 
       29.82         7.10         5.95        19.20        17.92        48.59 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6943 TCGA-CV-6951 
       60.49        54.74        90.12        20.52        19.79        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7103 
        6.08        53.95         7.13       111.16         5.26        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7247 
       12.92        21.80        71.21        77.16        47.47        18.97 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 
       36.13       210.97        89.33        22.85        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       34.09       100.57        56.48       153.86        16.64         6.38 
TCGA-CV-7446 TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.93         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A468 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-A6EP 
       15.25        10.42        34.36         2.53        11.44        13.94 
TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7596 
       12.10        58.45        30.94        33.86        14.04        11.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 TCGA-HD-8224 TCGA-HD-8634 
       21.63        20.25        12.62        13.38        14.66        12.66 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-P3-A6SW TCGA-P3-A6SX 
        3.65        15.95        11.54        14.37        36.82        47.01 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-T2-A6WZ TCGA-UF-A71B TCGA-UF-A7JJ 
       16.01        21.07         7.30        15.91        43.36        16.11 
TCGA-WA-A7H4 
       14.56 

   0 HIGH  LOW 
0.07 0.07 0.07 
     0   HIGH    LOW 
180.16 169.38 210.97 
    0  HIGH   LOW 
17.62 20.25 19.79 
[1] "0.1 - 180.2 (17.6)" "0.1 - 169.4 (20.2)" "0.1 - 211.0 (19.8)"
D1V2, continuous
      vv
clus   STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  0         14       44        39       116         7
  HIGH       3       15        12        72         2
  LOW        8       17        26        60         2
D1V3, multiclass
           clus
vv            0 HIGH LOW
  STAGE I    14    3   8
  STAGE II   44   15  17
  STAGE III  39   12  26
  STAGE IVA 116   72  60
  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       28 72 46 76
  HIGH     7 24 19 57
  LOW     13 35 33 35
D1V4, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 28    7  13
  T2    72   24  35
  T3    46   19  33
  T4    76   57  35
[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    95 27 78  4
  HIGH 41 15 41  1
  LOW  38 23 42  2
D1V5, multiclass
    clus
vv    0 HIGH LOW
  N0 95   41  38
  N1 27   15  23
  N2 78   41  42
  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     52 200
  HIGH  49  78
  LOW   38  89
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      52  200
  HIGH   49   78
  LOW    38   89
        clus
vv         0 HIGH LOW
  FEMALE  52   49  38
  MALE   200   78  89
[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                                      246
  HIGH                                   126
  LOW                                    126
      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
D1V7, multiclass
                                                             clus
vv                                                              0 HIGH LOW
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                       246  126 126
  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"
D1V8, binary
      cls
clus     0   1
  0     41 211
  HIGH  17 110
  LOW   25 102
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      41  211
  HIGH   17  110
  LOW    25  102
     clus
vv      0 HIGH LOW
  NO   41   17  25
  YES 211  110 102
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
D1V10, continuous
D1V11, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1     5                        24   216
  HIGH                                0     5                         6   114
  LOW                                 1     1                         6   111
D1V12, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   1
  ASIAN                              5    5   1
  BLACK OR AFRICAN AMERICAN         24    6   6
  WHITE                            216  114 111
[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     11 219
  HIGH   7 111
  LOW    7 115
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      11  219
  HIGH    7  111
  LOW     7  115
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      11    7   7
  NOT HISPANIC OR LATINO 219  111 115
[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   127  93
  FC.LOW.NONSIG 162  87
  FC.NEUTRAL     14  21
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          220           249            35 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           93            87            21 
$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        53.79        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        94.62         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        23.70        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4734 TCGA-CN-4735 TCGA-CN-4738 
       12.89        26.86        32.65        24.92        41.10        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5361 TCGA-CN-5364 TCGA-CN-5366 
       27.58        41.69         8.58        55.27        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        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 
       19.53         6.74         9.24        36.49        20.09        24.16 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        14.10        11.74        14.56        12.85        29.72 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A6V1 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 
        5.75         4.41         7.33         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        51.29        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       23.24        32.81        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-7370 TCGA-CR-7371 TCGA-CR-7373 
       39.16        40.93        35.84         3.45         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
        0.99        31.96        32.78        47.01        27.06        29.82 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5436 
       29.52        30.58         7.10        48.39       139.43        19.20 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 
      107.51        76.50        80.12        17.92        13.35        48.59 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       60.49        54.74         9.60         9.70         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
       26.43       126.08        19.79        42.38        30.08         6.08 
TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7102 
       10.98         2.50        64.83        18.81         7.99         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7252 
       52.31        12.92        21.80        77.16        18.97         4.96 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 
       36.13        57.47       210.97        89.33         0.46        22.85 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7435 
        0.07       100.57        14.89       156.49        19.76       153.86 
TCGA-CV-7438 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45U 
        6.38        35.93        27.98        24.99       169.38        35.47 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6K2 
        1.05        88.87         0.76        35.34         6.38        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6824 TCGA-D6-6826 
       10.42        10.55        18.84        34.36         2.53        11.44 
TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       12.36        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 
       35.54        33.86        14.04        12.10        11.18        21.63 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A76A 
       20.25        19.23        12.62        20.25        15.16         6.77 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       22.03        12.66        22.85         0.36        13.84         3.65 
TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61L TCGA-KU-A6H7 
       34.75        19.33        13.55         0.07        11.54        12.43 
TCGA-MT-A51W TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T3 
       14.37        12.62        17.98        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-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 
        9.34        12.43        12.72        16.96         6.87        32.45 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JO 
       13.25        13.68        44.65        62.27        16.11        20.75 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         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        57.44         4.01         7.76        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-4225 TCGA-BB-4228 
        2.27        11.05        20.48         6.15         4.60        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ 
       22.42        36.72        33.70        50.20        66.28        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81         6.28        12.69        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 
       40.44        21.11        12.99        20.55        43.73        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
       33.11        34.36        12.39        35.54         8.32        11.54 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 
       11.57        20.71        20.68        14.20        11.08        10.45 
TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T 
       12.95         3.68        35.01        17.59        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V6 
       17.29        15.91        12.07        10.09         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
        6.18        48.20        39.68        21.50        46.75        45.80 
TCGA-CQ-5332 TCGA-CQ-6222 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       10.42        66.28        34.75        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE 
       14.99        38.76        33.11        64.11        11.61        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        11.77        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6477 TCGA-CR-6482 
       26.27        58.42        50.01        39.52        16.90        11.34 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7372 
       12.46        11.51         9.27        47.18        47.34        24.95 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 
        9.17        34.06        19.92        17.13        12.89        31.10 
TCGA-CR-7393 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 
       29.85         5.13        35.41        29.95        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 
      108.95        76.24        17.95        94.88        91.53        23.05 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
       86.83         7.07        43.23        21.07        62.43         2.14 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6954 
        4.73        21.90        11.24        12.03        15.09        65.82 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 
        8.42        28.34         4.14       126.15        12.66         9.01 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       10.75       130.88         4.73        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       17.13        95.34        11.87        47.97         2.10        18.41 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 
       35.54        17.85         9.67        25.08         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A460 
       84.49         7.17        22.19       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 
       22.03         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-A6EO TCGA-DQ-5631 
       25.32        17.72        15.88         7.63        14.30        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 
       18.90        25.48        20.45         9.83        12.13        10.65 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       37.18         3.02        18.94         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       12.43        13.61        21.11         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        1.22         4.27         6.90        12.76        14.50        11.84 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
       14.47         5.29        11.84        13.35        18.15        10.75 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84         3.68        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 
       16.08        15.78        56.75        51.25        19.00        75.55 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       13.15        11.74        17.65        16.70        12.72        18.64 
TCGA-QK-A6VB TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       14.79         7.10        13.55        43.59        54.67         2.83 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       41.16        42.02        17.95        24.16        49.22        21.86 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       13.94        22.36        17.03 

$FC.NEUTRAL
TCGA-BA-6869 TCGA-CN-5373 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-A63W TCGA-CN-A642 
       21.17        22.45        19.07         9.07        11.44         2.70 
TCGA-CQ-7067 TCGA-CQ-A4CB TCGA-CR-7382 TCGA-CR-7391 TCGA-CR-7399 TCGA-CV-6933 
       16.73        29.36        26.17        30.02         5.95        90.12 
TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7238 
       53.95         7.13       111.16         5.26        71.21        47.47 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7437 TCGA-CV-7568 TCGA-CV-A45W 
       25.94        34.09        56.48        16.64        30.48        45.96 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6K1 TCGA-DQ-5629 TCGA-H7-7774 
        6.51        48.20        15.25        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        43.36 

  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        111.16 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       19.645        17.590        22.520 
[1] "0.1 - 211.0 (19.6)" "0.1 - 180.2 (17.6)" "2.7 - 111.2 (22.5)"
D2V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  FC.HIGH.SIG         8       26        31       118         3
  FC.LOW.NONSIG      13       44        39       116         7
  FC.NEUTRAL          4        6         7        14         1
D2V3, multiclass
           clus
vv          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I             8            13          4
  STAGE II           26            44          6
  STAGE III          31            39          7
  STAGE IVA         118           116         14
  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 81
  FC.LOW.NONSIG    27 72 46 76
  FC.NEUTRAL        6  8  8 11
D2V4, multiclass
       clus
vv      FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T0+T1          15            27          6
  T2             51            72          8
  T3             44            46          8
  T4             81            76         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   67 33 73  2
  FC.LOW.NONSIG 94 27 78  4
  FC.NEUTRAL    13  5 10  1
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0          67            94         13
  N1          33            27          5
  N2          73            78         10
  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    74 146
  FC.LOW.NONSIG  51 200
  FC.NEUTRAL     14  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     74  146
  FC.LOW.NONSIG   51  200
  FC.NEUTRAL      14   21
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE          74            51         14
  MALE           146           200         21
[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                                     218
  FC.LOW.NONSIG                                   245
  FC.NEUTRAL                                       35
               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
D2V7, multiclass
                                                             clus
vv                                                            FC.HIGH.SIG
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                               218
  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                                 245
  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                               35
  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"
D2V8, binary
               cls
clus              0   1
  FC.HIGH.SIG    38 182
  FC.LOW.NONSIG  41 210
  FC.NEUTRAL      4  31
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     38  182
  FC.LOW.NONSIG   41  210
  FC.NEUTRAL       4   31
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO           38            41          4
  YES         182           210         31
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, continuous
D2V10, continuous
D2V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.SIG                                  1     6
  FC.LOW.NONSIG                                1     5
  FC.NEUTRAL                                   0     0
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG                          11   196
  FC.LOW.NONSIG                        24   215
  FC.NEUTRAL                            1    30
D2V12, multiclass
                                  clus
vv                                 FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE           1             1          0
  ASIAN                                      6             5          0
  BLACK OR AFRICAN AMERICAN                 11            24          1
  WHITE                                    196           215         30
[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    11 198
  FC.LOW.NONSIG  11 218
  FC.NEUTRAL      3  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     11  198
  FC.LOW.NONSIG   11  218
  FC.NEUTRAL       3   29
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO              11            11          3
  NOT HISPANIC OR LATINO         198           218         29
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
