[1] "ofn"        "-oTBRCA-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/BRCA-TP/22506573/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BRCA-TP/22570937/APOBEC_clinical_corr_input_22572582/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=1097, in cluster file=978, common to both=977
[1]   2 977
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 750  111  116 
   0 HIGH  LOW 
 750  111  116 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           220              7            750 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           220              7            750 
[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_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 977 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=134,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=657,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	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=26,	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=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            2576    735    
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'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 977 columns, 1 survival variables, and 11 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"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=64, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
257 564 120  35 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
257 564 120  35 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
257 564 120  35 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
257 564 120  35 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
462 325 107  68 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
462 325 107  68 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
462 325 107  68 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
462 325 107  68 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=29, 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    634 109
  HIGH  92  16
  LOW  100  13
   0 HIGH  LOW 
 743  108  113 
   0 HIGH  LOW 
 109   16   13 
$`0`
TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A7-A0CD 
       19.20        63.12        36.13        88.60        19.56        38.30 
TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 
       23.61        24.26        21.73        22.32        11.28        11.97 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       11.05        53.06        29.03        33.01        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-AC-A5EI TCGA-AC-A62X TCGA-AO-A0JI 
        1.02        49.05        29.98        14.53        13.71        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         5.65         2.56        32.91        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I8 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        24.62        54.05        32.58 
TCGA-BH-A1F5 TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
       89.16        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LL-A440 TCGA-LL-A50Y TCGA-LL-A5YP 
       73.64        52.96        75.02        24.95        25.05        14.79 
TCGA-OL-A5RU TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ 
       40.08         8.52        14.37        43.43        14.27        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       31.79         7.96        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
      121.94        73.84        87.25       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D0 
       92.48        77.19         5.19        98.99        53.13        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       118.45        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        50.43        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YE 
       20.52        17.46        18.90        20.75        32.55        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT 
       50.47        21.90        49.48        18.61        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.47        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX 
       56.28        47.31        35.93        50.37        50.83        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC 
       34.29        35.47        30.61        37.45        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY 
       31.73        20.19        25.15        29.56        20.61        11.34 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SC TCGA-A7-A4SD TCGA-A7-A5ZV 
       10.29        13.41        14.70        14.66        14.50        12.10 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02        13.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        33.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05        10.98         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       45.07        18.05        13.02         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       12.00        37.05        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       40.01         9.99         9.99        12.00        50.04        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       22.95        73.91        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ 
       90.71        60.92        87.12        26.04        33.04        14.66 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        14.83        22.19        25.05        14.99 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       23.24        24.79        14.96         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        6.44         5.65         7.00         7.17         6.90         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.33         0.33         0.53         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33        80.28        81.63        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       58.95        32.78        21.40        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JJ 
       22.36        50.70        50.86        72.00        65.10        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       115.27       113.62       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       20.45        97.08        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TU TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       15.62        32.52        23.31        55.86        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN 
       83.87       134.14       125.16       101.00        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        41.82        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      105.30        50.96        98.76        98.66        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LO 
       85.64        71.05        86.53        54.21        63.62        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       40.54        33.30        38.96        10.59        77.62       281.29 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       32.58        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      146.50       112.37       233.62       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      140.88        68.45       234.28       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      140.28       282.90        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.55        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        74.99        18.84        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0B9 
       59.84        25.55        37.74        84.13        51.58        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       74.89        61.68        72.23        74.14        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        81.73        77.98        67.10        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
        4.41        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        2.37        16.96         2.50        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        90.84        26.66        72.56        37.74 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05         7.36        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.81        97.48        33.17        74.73       122.83        33.99 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63        53.98        55.50        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U 
       26.14        38.60        83.31        36.79        10.52       110.60 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
       18.64        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.16        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.59        12.92        12.49        11.34        11.28         0.16 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 
       12.95        12.33        12.36        15.45        16.87         9.76 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       24.56        12.95        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        13.48        55.50        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP 
       14.01        18.97        20.12        20.09        19.40        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       25.74        23.90        27.58        18.15        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        14.50        19.92        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31        16.64        12.99        15.16        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.14        17.42        16.04 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48        17.06         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.26        33.37        18.51        21.67 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       43.00        34.42        46.59        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       43.33        32.02        31.96        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.70        28.44        59.18         3.88 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX 
       28.90       102.61         8.75        43.04        52.73        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
        8.28        30.61        34.92        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       47.64        32.05        37.74        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56        12.33        29.72        38.07        32.91        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ 
       23.90        23.84        26.70        25.81        26.40        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        16.57        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG 
       30.08         7.86        18.90        13.94        10.52        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 
       19.96        55.00        52.73        25.91        22.09        17.52 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
        7.40       109.87       216.76        79.10        83.34        70.85 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       86.96       106.06       101.62        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       32.75        15.32        14.70        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.52        31.99        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       20.38        26.70        23.47        65.62        41.92 

$HIGH
TCGA-A2-A25A TCGA-A7-A26H TCGA-A8-A093 TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 
      107.70        23.80        17.95        45.07        16.57        19.79 
TCGA-AC-A5XS TCGA-BH-A0B6 TCGA-E2-A1LG TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-A1-A0SH 
       19.33        81.63        50.07        15.68        85.35        47.24 
TCGA-A1-A0SI TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0CR TCGA-A2-A0CX TCGA-A2-A0EQ 
       20.88       101.98        24.79       107.93        56.81        79.76 
TCGA-A2-A0EY TCGA-A2-A0SY TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A4RW TCGA-A7-A3IZ 
       63.29        44.28        21.67        19.33         7.30        10.59 
TCGA-A7-A56D TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08L TCGA-A8-A092 TCGA-A8-A095 
       14.73         1.02        43.00         9.99        30.97        41.98 
TCGA-A8-A09N TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2QI 
        1.02         0.99        19.23         5.72        22.26        19.33 
TCGA-AC-A3BB TCGA-AC-A3W7 TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XW TCGA-AO-A03M 
       32.45        15.48         7.96         0.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A0J4 TCGA-AO-A0J9 TCGA-AR-A0TX TCGA-AR-A2LE TCGA-B6-A0IK 
       66.77        52.18        53.03        64.83       166.42        18.77 
TCGA-B6-A0RV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0DX TCGA-BH-A0DZ 
      169.51        20.45        81.44        70.22        70.88        16.27 
TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W7 TCGA-BH-A18J TCGA-BH-A18P 
       23.90         5.85        13.61        44.81        20.12        30.28 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FN TCGA-BH-A208 
       51.39        51.16        12.00        25.08        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A2L8 TCGA-BH-A5J0 TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A1HM 
      130.16        20.12        23.51        11.77        12.66        12.33 
TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 
       20.25        12.95        16.70         0.03        14.43        33.99 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JN 
       19.20        14.17        17.49        16.50        15.78        20.38 
TCGA-D8-A27G TCGA-D8-A27V TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A152 TCGA-E2-A159 
       13.45        12.53        27.52        40.11        69.96        25.05 
TCGA-E2-A1IN TCGA-E2-A1LH TCGA-E2-A2P6 TCGA-E2-A574 TCGA-E9-A1R4 TCGA-EW-A1IW 
       22.19       106.75        34.55        38.76         6.12        12.20 
TCGA-EW-A1OV TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3E8 TCGA-GM-A2D9 TCGA-GM-A2DH 
       25.94        19.99         6.15        34.03        59.57        72.10 
TCGA-GM-A2DI TCGA-GM-A3NW TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-PE-A5DE 
       85.15       110.50        27.91        58.62        36.36        86.96 

$LOW
TCGA-A7-A26E TCGA-A8-A07E TCGA-A8-A084 TCGA-BH-A18H TCGA-E2-A2P5 TCGA-A1-A0SF 
       31.36        19.99        15.06        21.44        26.99        48.10 
TCGA-A1-A0SN TCGA-A2-A04X TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0YD TCGA-A2-A0YL 
       39.32        55.43        75.25       107.93        25.28        48.46 
TCGA-A2-A3XT TCGA-A7-A0DB TCGA-A7-A26G TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       91.07        33.11        23.74        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A8-A075 TCGA-A8-A07O TCGA-A8-A085 TCGA-A8-A08B 
       17.92        10.72        17.03         9.99        36.95        38.01 
TCGA-A8-A08P TCGA-A8-A097 TCGA-A8-A0A9 TCGA-AC-A2FO TCGA-AC-A5EH TCGA-AC-A62Y 
       31.00        12.00        27.02        74.14        16.80        17.42 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JE TCGA-AO-A129 
        7.59         7.04        44.42        21.53        76.77       108.03 
TCGA-AO-A12D TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AS 
       82.68        11.51        84.10       108.36       103.86        37.81 
TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A2LH 
      160.90       104.28       102.84        89.00        93.83        20.25 
TCGA-AR-A2LN TCGA-B6-A0I2 TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RT 
       38.17       143.38       165.76       255.68       212.25        89.46 
TCGA-B6-A0WZ TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AZ TCGA-BH-A0B3 
      206.86        37.87        68.12       103.63        63.09        39.55 
TCGA-BH-A0B4 TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0DH TCGA-BH-A0E1 TCGA-BH-A0EE 
       39.16        75.48        76.60        38.01        15.68        31.00 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A28O TCGA-BH-A42V 
       23.05        32.91        31.53       114.15        36.82        20.88 
TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HK 
       12.56        12.59        12.46        12.33        10.92        12.03 
TCGA-C8-A26W TCGA-D8-A13Y TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1XJ TCGA-D8-A1XM 
       12.53        56.81        18.15        20.09        21.83        17.69 
TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A14Y 
       14.24        13.05        37.51        40.96        34.26        69.34 
TCGA-E2-A14Z TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1LB TCGA-E9-A1NF 
       18.51        11.05        76.57        33.73        75.81        35.24 
TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A2JT TCGA-E9-A3QA 
       34.45        42.25        39.09        38.37         9.47        30.18 
TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A3U0 TCGA-GM-A2DL TCGA-GM-A3XL 
        0.79        39.72         8.48        17.49       115.69        69.30 
TCGA-JL-A3YX TCGA-LL-A5YL TCGA-LL-A5YO TCGA-PE-A5DC TCGA-PE-A5DD 
       11.57        17.06        14.47        47.01        64.21 

   0 HIGH  LOW 
0.16 0.03 0.79 
     0   HIGH    LOW 
282.90 169.51 255.68 
    0  HIGH   LOW 
30.61 23.85 34.45 
[1] "0.2 - 282.9 (30.6)" "0.0 - 169.5 (23.9)" "0.8 - 255.7 (34.5)"
D1V2, continuous
      vv
clus   STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  0         62       60        5        3       249       170         1
  HIGH      16        5        0        0        35        23         0
  LOW       10        6        1        1        42        34         1
      vv
clus   STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  0           105         20         47       12      10
  HIGH         20          3          5        2       0
  LOW          12          1          5        1       2
D1V3, multiclass
            clus
vv             0 HIGH LOW
  STAGE I     62   16  10
  STAGE IA    60    5   6
  STAGE IB     5    0   1
  STAGE II     3    0   1
  STAGE IIA  249   35  42
  STAGE IIB  170   23  34
  STAGE III    1    0   1
  STAGE IIIA 105   20  12
  STAGE IIIB  20    3   1
  STAGE IIIC  47    5   5
  STAGE IV    12    2   1
  STAGE X     10    0   2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus    T1  T2  T3  T4
  0    207 429  86  28
  HIGH  27  59  20   5
  LOW   23  76  14   2
D1V4, multiclass
    clus
vv     0 HIGH LOW
  T1 207   27  23
  T2 429   59  76
  T3  86   20  14
  T4  28    5   2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus    N0  N1  N2  N3
  0    347 250  84  56
  HIGH  58  29  17   5
  LOW   57  46   6   7
D1V5, multiclass
    clus
vv     0 HIGH LOW
  N0 347   58  57
  N1 250   29  46
  N2  84   17   6
  N3  56    5   7
[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    647  13
  HIGH  93   2
  LOW  102   1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     647   13
  HIGH   93    2
  LOW   102    1
   clus
vv    0 HIGH LOW
  0 647   93 102
  1  13    2   1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
      cls
clus     0   1
  0    743   7
  HIGH 111   0
  LOW  114   2
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     743    7
  HIGH  111    0
  LOW   114    2
        clus
vv         0 HIGH LOW
  FEMALE 743  111 114
  MALE     7    0   2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
      cls
clus     0   1
  0    293 394
  HIGH  46  47
  LOW   48  61
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     293  394
  HIGH   46   47
  LOW    48   61
     clus
vv      0 HIGH LOW
  NO  293   46  48
  YES 394   47  61
[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   INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  0                             1                           554
  HIGH                          0                            75
  LOW                           0                            82
      vv
clus   INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA
  0                               117                   1                     5
  HIGH                             33                   1                     0
  LOW                              22                   3                     1
      vv
clus   MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER, SPECIFY
  0                                  22                 14             36
  HIGH                                1                  0              1
  LOW                                 4                  0              3
D1V9, multiclass
                                  clus
vv                                   0 HIGH LOW
  INFILTRATING CARCINOMA NOS         1    0   0
  INFILTRATING DUCTAL CARCINOMA    554   75  82
  INFILTRATING LOBULAR CARCINOMA   117   33  22
  MEDULLARY CARCINOMA                1    1   3
  METAPLASTIC CARCINOMA              5    0   1
  MIXED HISTOLOGY (PLEASE SPECIFY)  22    1   4
  MUCINOUS CARCINOMA                14    0   0
  OTHER, SPECIFY                    36    1   3
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
      vv
clus   AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0                                   1    33                        86   561
  HIGH                                0    11                        15    72
  LOW                                 0    13                        20    72
D1V11, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   0
  ASIAN                             33   11  13
  BLACK OR AFRICAN AMERICAN         86   15  20
  WHITE                            561   72  72
[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"
D1V12, binary
      cls
clus     0   1
  0     28 593
  HIGH   4  85
  LOW    2  94
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      28  593
  HIGH    4   85
  LOW     2   94
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      28    4   2
  NOT HISPANIC OR LATINO 593   85  94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH 187  28
  FC.LOW.ENRICH    5   1
  FC.NO.ENRICH   634 109
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
           215              6            743 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            28              1            109 
$FC.HIGH.ENRICH
TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A26H TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A093 
      107.70        31.36        23.80        19.99        15.06        17.95 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-BH-A0B6 TCGA-BH-A18H 
       45.07        16.57        19.79        19.33        81.63        21.44 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-A1-A0SF TCGA-A1-A0SH 
       50.07        26.99        15.68        85.35        48.10        47.24 
TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CR 
       20.88        39.32       101.98        55.43        24.79       107.93 
TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SY 
       75.25       107.93        56.81        79.76        63.29        44.28 
TCGA-A2-A0YD TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A3XT TCGA-A2-A4RW 
       25.28        21.67        19.33        48.46        91.07         7.30 
TCGA-A7-A0DB TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       33.11        23.74        10.59        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A8-A06Q TCGA-A8-A075 TCGA-A8-A07B 
       17.92        14.73        10.72         1.02        17.03        43.00 
TCGA-A8-A07O TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A092 
        9.99        36.95        38.01         9.99        31.00        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09N TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C 
       41.98        12.00         1.02         0.99        27.02        19.23 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3W7 
        5.72        22.26        74.14        19.33        32.45        15.48 
TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XW TCGA-AO-A03M 
       16.80        17.42         7.96         0.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JE 
       66.77        44.42        52.18        53.03        21.53        76.77 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A0TX TCGA-AR-A1AI 
      108.03        82.68        11.51        84.10        64.83       108.36 
TCGA-AR-A1AK TCGA-AR-A1AS TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A2LE 
      103.86        37.81       104.28       102.84        89.00       166.42 
TCGA-AR-A2LH TCGA-AR-A2LN TCGA-B6-A0I2 TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RE 
       20.25        38.17       143.38        18.77       165.76       255.68 
TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WZ TCGA-B6-A3ZX TCGA-B6-A408 
      212.25        89.46       169.51       206.86        37.87        68.12 
TCGA-B6-A40B TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
      103.63        20.45        63.09        81.44        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0DZ 
       70.22        75.48        76.60        38.01        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0EE TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W7 TCGA-BH-A0WA 
       15.68        31.00         5.85        13.61        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EV 
       32.91        20.12        30.28        51.39        51.16        12.00 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A209 
       31.53        25.08       114.15        72.07        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42V TCGA-BH-A5J0 TCGA-C8-A12P TCGA-C8-A12Q 
       36.82        20.12        20.88        23.51        11.77        12.66 
TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HK 
       12.56        12.59        12.46        12.33        10.92        12.03 
TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A275 
       12.33        20.25        12.53        12.95        16.70         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.43        33.99        56.81        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1XM 
       16.50        15.78        18.15        20.09        20.38        17.69 
TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27V TCGA-E2-A108 TCGA-E2-A10B 
       14.24        13.45        13.05        12.53        27.52        37.51 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 
       40.11        40.96        34.26        69.34        18.51        69.96 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1LB 
       25.05        11.05        76.57        33.73        22.19        75.81 
TCGA-E2-A1LH TCGA-E2-A2P6 TCGA-E2-A574 TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A226 
      106.75        34.55        38.76        35.24         6.12        34.45 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A2JT TCGA-E9-A3QA TCGA-E9-A5FL 
       42.25        39.09        38.37         9.47        30.18         0.79 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1OV TCGA-EW-A1PB TCGA-EW-A1PC 
       12.20        39.72         8.48        25.94        19.99         6.15 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-GM-A2D9 TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL 
       34.03        17.49        59.57        72.10        85.15       115.69 
TCGA-GM-A3NW TCGA-GM-A3XL TCGA-JL-A3YX TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LQ-A4E4 
      110.50        69.30        11.57        17.06        14.47        27.91 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       58.62        36.36        47.01        64.21        86.96 

$FC.LOW.ENRICH
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AR-A24H TCGA-AR-A256 TCGA-BH-A0HF TCGA-D8-A1XJ 
        7.59         7.04       160.90        93.83        23.90        21.83 

$FC.NO.ENRICH
TCGA-A1-A0SP TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A7-A0CD 
       19.20        63.12        36.13        88.60        19.56        38.30 
TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 
       23.61        24.26        21.73        22.32        11.28        11.97 
TCGA-A7-A5ZX TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A091 
       11.05        53.06        29.03        33.01        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-AC-A5EI TCGA-AC-A62X TCGA-AO-A0JI 
        1.02        49.05        29.98        14.53        13.71        50.24 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A1AM TCGA-AR-A1AR 
       17.79         5.65         2.56        32.91        98.33        17.23 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I8 TCGA-BH-A0DO TCGA-BH-A0EA 
       66.15        57.27        73.35        24.62        54.05        32.58 
TCGA-BH-A1F5 TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A158 TCGA-E2-A15O TCGA-E2-A1BC 
       89.16        10.42        21.14        14.79        50.79        16.47 
TCGA-E2-A1L8 TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LL-A440 TCGA-LL-A50Y TCGA-LL-A5YP 
       73.64        52.96        75.02        24.95        25.05        14.79 
TCGA-OL-A5RU TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ 
       40.08         8.52        14.37        43.43        14.27        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       31.79         7.96        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
      121.94        73.84        87.25       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D0 
       92.48        77.19         5.19        98.99        53.13        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72       134.40 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       118.45        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        50.43        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YE 
       20.52        17.46        18.90        20.75        32.55        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT 
       50.47        21.90        49.48        18.61        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.47        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX 
       56.28        47.31        35.93        50.37        50.83        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC 
       34.29        35.47        30.61        37.45        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26J TCGA-A7-A3IY 
       31.73        20.19        25.15        29.56        20.61        11.34 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SC TCGA-A7-A4SD TCGA-A7-A5ZV 
       10.29        13.41        14.70        14.66        14.50        12.10 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02        13.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        33.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05        10.98         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       45.07        18.05        13.02         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       12.00        37.05        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09M 
       40.01         9.99         9.99        12.00        50.04        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       22.95        73.91        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ 
       90.71        60.92        87.12        26.04        33.04        14.66 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        14.83        22.19        25.05        14.99 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       23.24        24.79        14.96         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        6.44         5.65         7.00         7.17         6.90         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.33         0.33         0.53         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33        80.28        81.63        95.70        68.75        69.83 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       58.95        32.78        21.40        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JJ 
       22.36        50.70        50.86        72.00        65.10        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       115.27       113.62       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      102.31        98.27        70.42        60.56        53.88        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       20.45        97.08        82.62        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TU TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       15.62        32.52        23.31        55.86        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN 
       83.87       134.14       125.16       101.00        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        41.82        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      105.30        50.96        98.76        98.66        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LO 
       85.64        71.05        86.53        54.21        63.62        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       40.54        33.30        38.96        10.59        77.62       281.29 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       32.58        11.90       275.87       129.57        50.70        65.52 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      146.50       112.37       233.62       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      140.88        68.45       234.28       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      140.28       282.90        97.48       188.68        79.46        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.01       113.79       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.55        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        74.99        18.84        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0B9 
       59.84        25.55        37.74        84.13        51.58        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       74.89        61.68        72.23        74.14        85.87        77.75 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        74.14        41.75        46.39        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        81.73        77.98        67.10        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        79.00        67.86 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EB 
        4.41        14.30         9.63        44.81        81.83        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       63.32        30.35        10.78        15.16        63.39        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        2.37        16.96         2.50        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        90.84        26.66        72.56        37.74 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05         7.36        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       25.81        97.48        33.17        74.73       122.83        33.99 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63        53.98        55.50        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U 
       26.14        38.60        83.31        36.79        10.52       110.60 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
       18.64        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.16        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.59        12.92        12.49        11.34        11.28         0.16 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 
       12.95        12.33        12.36        15.45        16.87         9.76 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       24.56        12.95        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        13.48        55.50        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP 
       14.01        18.97        20.12        20.09        19.40        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       25.74        23.90        27.58        18.15        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        14.50        19.92        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31        16.64        12.99        15.16        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.14        17.42        16.04 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48        17.06         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.26        33.37        18.51        21.67 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       43.00        34.42        46.59        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       43.33        32.02        31.96        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.70        28.44        59.18         3.88 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        19.66        24.59 
TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX 
       28.90       102.61         8.75        43.04        52.73        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
        8.28        30.61        34.92        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       47.64        32.05        37.74        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56        12.33        29.72        38.07        32.91        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ 
       23.90        23.84        26.70        25.81        26.40        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        16.57        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG 
       30.08         7.86        18.90        13.94        10.52        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 
       19.96        55.00        52.73        25.91        22.09        17.52 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
        7.40       109.87       216.76        79.10        83.34        70.85 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       86.96       106.06       101.62        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       32.75        15.32        14.70        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.52        31.99        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       20.38        26.70        23.47        65.62        41.92 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
          0.03           7.04           0.16 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        255.68         160.90         282.90 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        31.000         22.865         30.610 
[1] "0.0 - 255.7 (31.0)" "7.0 - 160.9 (22.9)" "0.2 - 282.9 (30.6)"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FC.HIGH.ENRICH      26       10        1        1        73        56
  FC.LOW.ENRICH        0        1        0        0         4         1
  FC.NO.ENRICH        62       60        5        3       249       170
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  FC.HIGH.ENRICH         1         31          4         10        3       2
  FC.LOW.ENRICH          0          1          0          0        0       0
  FC.NO.ENRICH           1        105         20         47       12      10
D2V3, multiclass
            clus
vv           FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  STAGE I                26             0           62
  STAGE IA               10             1           60
  STAGE IB                1             0            5
  STAGE II                1             0            3
  STAGE IIA              73             4          249
  STAGE IIB              56             1          170
  STAGE III               1             0            1
  STAGE IIIA             31             1          105
  STAGE IIIB              4             0           20
  STAGE IIIC             10             0           47
  STAGE IV                3             0           12
  STAGE X                 2             0           10
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FC.HIGH.ENRICH  49 130  33   7
  FC.LOW.ENRICH    1   5   1   0
  FC.NO.ENRICH   207 429  86  28
D2V4, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  T1             49             1          207
  T2            130             5          429
  T3             33             1           86
  T4              7             0           28
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FC.HIGH.ENRICH 110  73  23  12
  FC.LOW.ENRICH    5   2   0   0
  FC.NO.ENRICH   347 250  84  56
D2V5, multiclass
    clus
vv   FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  N0            110             5          347
  N1             73             2          250
  N2             23             0           84
  N3             12             0           56
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus               0   1
  FC.HIGH.ENRICH 189   3
  FC.LOW.ENRICH    6   0
  FC.NO.ENRICH   647  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  189    3
  FC.LOW.ENRICH     6    0
  FC.NO.ENRICH    647   13
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0            189             6          647
  1              3             0           13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus               0   1
  FC.HIGH.ENRICH 218   2
  FC.LOW.ENRICH    7   0
  FC.NO.ENRICH   743   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH  218    2
  FC.LOW.ENRICH     7    0
  FC.NO.ENRICH    743    7
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE            218             7          743
  MALE                2             0            7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                cls
clus               0   1
  FC.HIGH.ENRICH  90 106
  FC.LOW.ENRICH    4   2
  FC.NO.ENRICH   293 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH   90  106
  FC.LOW.ENRICH     4    2
  FC.NO.ENRICH    293  394
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO              90             4          293
  YES            106             2          394
[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             INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  FC.HIGH.ENRICH                          0                           152
  FC.LOW.ENRICH                           0                             5
  FC.NO.ENRICH                            1                           554
                vv
clus             INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  FC.HIGH.ENRICH                             54                   4
  FC.LOW.ENRICH                               1                   0
  FC.NO.ENRICH                              117                   1
                vv
clus             METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  FC.HIGH.ENRICH                     1                                5
  FC.LOW.ENRICH                      0                                0
  FC.NO.ENRICH                       5                               22
                vv
clus             MUCINOUS CARCINOMA OTHER, SPECIFY
  FC.HIGH.ENRICH                  0              3
  FC.LOW.ENRICH                   0              1
  FC.NO.ENRICH                   14             36
D2V9, multiclass
                                  clus
vv                                 FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  INFILTRATING CARCINOMA NOS                    0             0            1
  INFILTRATING DUCTAL CARCINOMA               152             5          554
  INFILTRATING LOBULAR CARCINOMA               54             1          117
  MEDULLARY CARCINOMA                           4             0            1
  METAPLASTIC CARCINOMA                         1             0            5
  MIXED HISTOLOGY (PLEASE SPECIFY)              5             0           22
  MUCINOUS CARCINOMA                            0             0           14
  OTHER, SPECIFY                                3             1           36
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FC.HIGH.ENRICH                                0    24
  FC.LOW.ENRICH                                 0     0
  FC.NO.ENRICH                                  1    33
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH                        35   138
  FC.LOW.ENRICH                          0     6
  FC.NO.ENRICH                          86   561
D2V11, multiclass
                                  clus
vv                                 FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  AMERICAN INDIAN OR ALASKA NATIVE              0             0            1
  ASIAN                                        24             0           33
  BLACK OR AFRICAN AMERICAN                    35             0           86
  WHITE                                       138             6          561
[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"
D2V12, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   6 175
  FC.LOW.ENRICH    0   4
  FC.NO.ENRICH    28 593
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    6  175
  FC.LOW.ENRICH     0    4
  FC.NO.ENRICH     28  593
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  6             0           28
  NOT HISPANIC OR LATINO            175             4          593
[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"
