[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/19775058/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/BRCA-TP/20231607/APOBEC_clinical_corr_input_20231679/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=1098, in cluster file=978, common to both=977
[1]   2 977
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 750  133   94 
   0 HIGH  LOW 
 750  133   94 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          220           656           101 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          220           656           101 
[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=132,	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=689,	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=13,	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=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=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=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
258 563 119  35 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
258 563 119  35 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
258 563 119  35 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
258 563 119  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    634 108
  HIGH 110  19
  LOW   81  10
   0 HIGH  LOW 
 742  129   91 
   0 HIGH  LOW 
 108   19   10 
$`0`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK 
        8.52        14.37        43.43        14.27        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CK 
      121.94        73.84        87.25        63.12        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU 
       99.12       114.81        92.48        88.60        77.19         5.19 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       98.99        53.13        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       118.45        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        50.43        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       20.75        32.55        18.21        50.47        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.37        50.83        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       35.47        30.61        37.45        35.67        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26I 
       20.19        25.15        23.61        29.56        24.26        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SC TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A7-A5ZX 
       14.70        11.97        14.66        14.50        12.10        11.05 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02        13.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        33.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        12.00        32.05        10.98         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       24.99         9.99        45.07        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08R 
       33.01        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A099 
       33.01       112.08        43.00        40.01        33.01         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
        9.99        12.00         1.02        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB 
       14.01        12.00        19.04        13.02        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       38.04        22.95        73.91        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        26.04        33.04 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM 
       14.66         6.48        16.31        14.83        22.19        25.05 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AC-A62X 
       14.99        23.24        24.79        14.53        14.96        13.71 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.33         0.33         0.33         6.44         5.65         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.90         0.36         0.33         0.33         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.53         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O 
        0.33         0.33         0.33         5.33        80.28        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
       95.70        68.75        47.87        58.95        32.78        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC 
       26.04        37.48        20.32        22.36        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       72.00        65.10        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
      115.27        99.25       108.72       106.78        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TU TCGA-AR-A0TY 
       15.62        32.52         2.56        32.91        23.31        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       133.22        83.87       134.14       125.16       101.00 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        41.82        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
        2.76       112.77        97.84       105.27       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        99.62        93.30        85.64        71.05 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        66.15        63.62        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
      281.29        32.58        24.62        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37       233.62       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN 
       84.59       129.07       140.88        68.45       234.28       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       102.77       140.48       282.90        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        18.35        21.47       113.79       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
      139.17       170.17         7.07        85.35        70.16        18.84 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B7 
       71.15        62.93        59.84        25.55        37.74        84.13 
TCGA-BH-A0B8 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       51.58        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       61.51        21.70        74.89        61.68        72.23        74.14 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        77.95        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       29.98        13.91        78.28        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
        2.56        38.47        67.86         4.41        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        24.49        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN 
       41.00        52.96        26.50        20.38         2.37        16.96 
TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18G TCGA-BH-A18I 
        5.59        23.93        24.95        42.35         4.90        35.93 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        26.66        72.56        37.74        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       42.28        55.69        49.58        17.69        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       97.48        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ 
       38.60        83.31         6.44        10.52       109.28        18.64 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66        48.53         3.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
       12.92         4.08        11.34        11.28         0.16        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 
       12.95        12.33        12.36         8.28         9.67         9.50 
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-A146 TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        13.48        21.14        55.50        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       53.00        14.01        18.97        20.12        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        14.50        19.92        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        15.52         9.93        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       16.04        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        10.09        13.08        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E 
       21.67        43.00        34.42        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A153 
       75.98        43.33        32.02        31.96        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE 
       54.18        60.36        73.64        19.66        24.59        28.90 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04        52.73        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       30.61        34.92        34.82        32.88        36.82        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       36.20        36.56        39.55        41.62        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       32.05        37.74        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       12.33        29.72        38.07        32.91        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ TCGA-EW-A1J1 
       23.84        26.70        25.81        26.40        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       13.25        16.57        28.77        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        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        10.16 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40       109.87       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XG 
       70.85        86.96       106.06       101.62        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.47 
TCGA-JL-A3YW TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN 
       11.84        24.95        32.75        25.05        15.32        14.70 
TCGA-LL-A5YP TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.79        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       26.70        23.47        65.62        41.92 

$HIGH
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0CR TCGA-A2-A0CX 
       47.24        20.88       101.98        24.79       107.93        56.81 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SY TCGA-A2-A0YD TCGA-A2-A0YH TCGA-A2-A0YK 
       79.76        63.29        44.28        25.28        21.67        19.33 
TCGA-A2-A25A TCGA-A2-A4RW TCGA-A7-A26H TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A56D 
      107.70         7.30        23.80        10.59        14.93        14.73 
TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08L TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        1.02        43.00         9.99        30.97        17.95        41.98 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 
       45.07         1.02         0.99         0.95         5.72         1.48 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A5XS 
       19.33        32.45        16.57        19.79        15.48        19.33 
TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A0J4 
        7.96         0.33         5.59        61.35        66.77        52.18 
TCGA-AO-A0J9 TCGA-AR-A0TX TCGA-AR-A1AK TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LE 
       53.03        64.83       103.86       104.28        93.83       166.42 
TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RV TCGA-B6-A0WZ TCGA-BH-A0AW TCGA-BH-A0B0 
       18.77       255.68       157.41       206.86        20.45        81.44 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BP TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0EE 
       70.22        81.63        75.48        70.88        16.27        31.00 
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        24.62        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A2L8 TCGA-BH-A5J0 TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A1HE 
      130.16        20.12        23.51        11.77        12.66        12.33 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 
       12.03        12.33        20.25        12.53        12.95         9.53 
TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
        0.03        14.43        33.99        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A27G TCGA-D8-A27H 
       16.50        15.78        20.09        20.38        13.45        13.05 
TCGA-D8-A27V TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A152 TCGA-E2-A159 
       12.53        27.52        40.11        40.96        69.96        25.05 
TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 
       33.73        22.19        75.81        50.07       106.75        26.99 
TCGA-E2-A2P6 TCGA-E2-A574 TCGA-E9-A1R4 TCGA-E9-A3QA TCGA-EW-A1IW TCGA-EW-A1J5 
       34.55        38.76         6.12        30.18        12.20        15.68 
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-A2DO TCGA-GM-A3NW TCGA-LL-A5YL TCGA-LQ-A4E4 TCGA-OL-A5DA 
       85.15        85.35       110.50        17.06        27.91        58.62 
TCGA-OL-A5RW TCGA-PE-A5DD TCGA-PE-A5DE 
       36.36        64.21        86.96 

$LOW
TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A04X TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0YL 
       48.10        39.32        55.43        75.25       107.93        48.46 
TCGA-A2-A3XT TCGA-A7-A0DB TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A4SB TCGA-A7-A4SE 
       91.07        33.11        31.36        23.74        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07O TCGA-A8-A084 
       17.92        10.72        17.03        19.99         9.99        15.06 
TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A097 TCGA-A8-A0A9 TCGA-AC-A2FO 
       36.95        38.01        31.00        12.00        27.02        74.14 
TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AO-A03V TCGA-AO-A0JA 
       16.80        17.42         7.59         7.04        29.13        21.53 
TCGA-AO-A0JE TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A1KS TCGA-AR-A0TS TCGA-AR-A1AI 
       76.77       108.03        64.04         0.53        84.10       108.36 
TCGA-AR-A1AS TCGA-AR-A24H TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A2LH TCGA-AR-A2LN 
       37.81       160.90        77.69        89.00        20.25        38.17 
TCGA-B6-A0I2 TCGA-B6-A0IO TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A3ZX TCGA-B6-A408 
      143.38       165.76       212.25        89.46        37.87        68.12 
TCGA-B6-A40B TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0BR TCGA-BH-A0DH 
      103.63        63.09        39.55        39.16        76.60        38.01 
TCGA-BH-A0E1 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A28O 
       15.68        23.05        32.91        31.53       114.15        10.65 
TCGA-BH-A42V TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HF TCGA-D8-A13Y 
       20.88        12.56         1.87         4.11        10.92        56.81 
TCGA-D8-A1JD TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-E2-A10B TCGA-E2-A14V 
       18.15        21.80        17.69        14.24        37.51        34.26 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E9-A1NF TCGA-E9-A226 
       69.34        18.51        11.05        76.57        35.24        34.45 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A2JT TCGA-E9-A5FL TCGA-EW-A1IX 
       42.25        39.09        38.37         9.47         0.79        39.72 
TCGA-EW-A1IY TCGA-EW-A3U0 TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YX TCGA-LL-A5YO 
        8.48        17.49       115.69        69.30        11.57        14.47 
TCGA-PE-A5DC 
       47.01 

   0 HIGH  LOW 
0.16 0.03 0.53 
     0   HIGH    LOW 
282.90 255.68 212.25 
     0   HIGH    LOW 
30.215 25.050 34.450 
[1] "0.2 - 282.9 (30.2)" "0.0 - 255.7 (25.1)" "0.5 - 212.2 (34.5)"
D1V2, continuous
      vv
clus   STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  0         61       62        5        3       250       169         1
  HIGH      19        5        0        1        41        32         0
  LOW        7        6        1        0        36        25         1
      vv
clus   STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  0           104         22         47       12         1      10
  HIGH         20          3          7        2         0       1
  LOW          12          1          3        1         0       1
D1V3, multiclass
            clus
vv             0 HIGH LOW
  STAGE I     61   19   7
  STAGE IA    62    5   6
  STAGE IB     5    0   1
  STAGE II     3    1   0
  STAGE IIA  250   41  36
  STAGE IIB  169   32  25
  STAGE III    1    0   1
  STAGE IIIA 104   20  12
  STAGE IIIB  22    3   1
  STAGE IIIC  47    7   3
  STAGE IV    12    2   1
  STAGE TIS    1    0   0
  STAGE X     10    1   1
[1] 13  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    208 428  85  28
  HIGH  30  74  23   5
  LOW   20  61  11   2
D1V4, multiclass
    clus
vv     0 HIGH LOW
  T1 208   30  20
  T2 428   74  61
  T3  85   23  11
  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  71  36  17   7
  LOW   44  39   6   5
D1V5, multiclass
    clus
vv     0 HIGH LOW
  N0 347   71  44
  N1 250   36  39
  N2  84   17   6
  N3  56    7   5
[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    646  13
  HIGH 114   2
  LOW   81   1
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     646   13
  HIGH  114    2
  LOW    81    1
   clus
vv    0 HIGH LOW
  0 646  114  81
  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 133   0
  LOW   92   2
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     743    7
  HIGH  133    0
  LOW    92    2
        clus
vv         0 HIGH LOW
  FEMALE 743  133  92
  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    285 371
  HIGH  55  53
  LOW   37  48
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     285  371
  HIGH   55   53
  LOW    37   48
     clus
vv      0 HIGH LOW
  NO  285   55  37
  YES 371   53  48
[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                           555
  HIGH                          0                            89
  LOW                           0                            68
      vv
clus   INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA METAPLASTIC CARCINOMA
  0                               116                   1                     5
  HIGH                             40                   2                     0
  LOW                              15                   2                     1
      vv
clus   MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  0                                  21                 14             37
  HIGH                                1                  0              1
  LOW                                 4                  0              3
D1V9, multiclass
                                  clus
vv                                   0 HIGH LOW
  INFILTRATING CARCINOMA NOS         1    0   0
  INFILTRATING DUCTAL CARCINOMA    555   89  68
  INFILTRATING LOBULAR CARCINOMA   116   40  15
  MEDULLARY CARCINOMA                1    2   2
  METAPLASTIC CARCINOMA              5    0   1
  MIXED HISTOLOGY (PLEASE SPECIFY)  21    1   4
  MUCINOUS CARCINOMA                14    0   0
  OTHER  SPECIFY                    37    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    16                        19    85
  LOW                                 0     8                        16    59
D1V11, multiclass
                                  clus
vv                                   0 HIGH LOW
  AMERICAN INDIAN OR ALASKA NATIVE   1    0   0
  ASIAN                             33   16   8
  BLACK OR AFRICAN AMERICAN         86   19  16
  WHITE                            561   85  59
[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   4 104
  LOW    2  75
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      28  593
  HIGH    4  104
  LOW     2   75
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO      28    4   2
  NOT HISPANIC OR LATINO 593  104  75
[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   186  28
  FC.LOW.NONSIG 555  94
  FC.NEUTRAL     84  15
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
          214           649            99 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
           28            94            15 
$FC.HIGH.SIG
TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A04X 
       48.10        47.24        20.88        39.32       101.98        55.43 
TCGA-A2-A0CM TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0EQ 
       24.79       107.93        75.25       107.93        56.81        79.76 
TCGA-A2-A0EY TCGA-A2-A0SY TCGA-A2-A0YD TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL 
       63.29        44.28        25.28        21.67        19.33        48.46 
TCGA-A2-A25A TCGA-A2-A3XT TCGA-A2-A4RW TCGA-A7-A0DB TCGA-A7-A26E TCGA-A7-A26G 
      107.70        91.07         7.30        33.11        31.36        23.74 
TCGA-A7-A26H TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       23.80        10.59        14.93        13.74        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A8-A06Q TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       14.73        10.72         1.02        17.03        43.00        19.99 
TCGA-A8-A07O TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P 
        9.99        15.06        36.95        38.01         9.99        31.00 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N 
       30.97        17.95        41.98        12.00        45.07         1.02 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FO 
        0.99        27.02         0.95         5.72         1.48        74.14 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A5EH 
       19.33        32.45        16.57        19.79        15.48        16.80 
TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XW TCGA-AO-A03M 
       19.33        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        29.13        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        64.04         0.53        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        77.69        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       157.41       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-A0B6 TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0DH TCGA-BH-A0DX 
       70.22        81.63        75.48        76.60        38.01        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0EE TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W7 
       16.27        15.68        31.00         5.85        13.61        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18U TCGA-BH-A18V 
       23.05        32.91        20.12        30.28        51.39        51.16 
TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A208 
       12.00        31.53        24.62       114.15        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42V TCGA-BH-A5J0 TCGA-C8-A12P 
      130.16        10.65        20.12        20.88        23.51        11.77 
TCGA-C8-A12Q TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.66        12.56         1.87         4.11        12.33        10.92 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 
       12.03        12.33        20.25        12.53        12.95         9.53 
TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J8 
        0.03        14.43        33.99        56.81        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1JN 
       17.49        16.50        15.78        18.15        20.09        20.38 
TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27V TCGA-E2-A108 
       17.69        14.24        13.45        13.05        12.53        27.52 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A14Z 
       37.51        40.11        40.96        34.26        69.34        18.51 
TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1IN 
       69.96        25.05        11.05        76.57        33.73        22.19 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A574 
       75.81        50.07       106.75        26.99        34.55        38.76 
TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B 
       35.24         6.12        34.45        42.25        39.09        38.37 
TCGA-E9-A2JT TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        9.47        30.18         0.79        12.20        39.72         8.48 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3E8 TCGA-EW-A3U0 
       15.68        25.94        19.99         6.15        34.03        17.49 
TCGA-GM-A2D9 TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DO TCGA-GM-A3NW 
       59.57        72.10        85.15       115.69        85.35       110.50 
TCGA-GM-A3XL TCGA-JL-A3YX TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LQ-A4E4 TCGA-OL-A5DA 
       69.30        11.57        17.06        14.47        27.91        58.62 
TCGA-OL-A5RW TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       36.36        47.01        64.21        86.96 

$FC.LOW.NONSIG
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SP 
        8.52        14.37        14.27        31.79         7.96        19.20 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CP 
      143.15        18.02        78.41        73.84        87.25        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D0 
       88.60        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        89.36 
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-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T0 
       31.82        61.94        54.64        27.12        50.43        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       20.75        32.55        18.21        50.47        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E 
       22.45        20.25        19.20        42.44        17.19       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        36.23        33.93        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       47.31        35.93        50.83        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       30.61        35.67        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 
       29.56        24.26        21.73        22.32        11.34        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SC TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.66        14.50 
TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       12.10        11.05        13.02        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        33.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W 
       18.97        14.01        32.05        10.98         8.98         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       45.07        13.02         0.99        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       37.05        31.00         0.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       40.01         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       49.05        29.98        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BK 
       21.04        17.03        38.04        22.95        73.91        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ 
       99.35        40.57        87.12        26.04        33.04        14.66 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ 
        6.48        16.31        22.19        14.99        23.24        24.79 
TCGA-AC-A62X TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
       13.71         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.33         0.33         0.33         6.44         5.65         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.90         0.36         0.33         0.33         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.53         5.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        0.33         5.33        80.28        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       47.87        32.78        21.40        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ 
       22.36        50.70        72.00        65.10        50.24        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        99.25       108.72       106.78 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       98.27        57.30        48.36        40.57        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TU TCGA-AR-A0TY 
       15.62        32.52         2.56        32.91        23.31        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       133.22        83.87       134.14       125.16       101.00 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       97.68        98.33        96.00        93.90        99.32        17.23 
TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K 
       41.82        94.29        61.28        86.53        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       94.22       120.33        99.78       118.59         2.76       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84       105.27       105.30        32.58        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LJ TCGA-AR-A2LK 
       99.62        93.30        85.64        71.05        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       66.15        63.62        39.39        40.54        57.27        73.35 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I6 
       33.30        38.96        10.59        77.62       281.29        32.58 
TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       24.62        12.13       275.87       129.57        50.70        65.72 
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-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY 
      282.90        97.48       188.68        79.63        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.88        43.59 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
       73.51       139.17       170.17         7.07        85.35        70.16 
TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B7 
       18.84        71.15        59.84        25.55        37.74        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       74.89        61.68        74.14        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        49.05        41.75        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       45.83        77.98        23.44        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E2 
       15.65         3.22         2.56        38.47         4.41        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
        9.63        44.81        46.19        32.58        24.49        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 
       30.35        10.78        15.16        37.78        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         2.37         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18L 
       23.93        24.95        42.35         4.90        35.93        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        37.74        55.63        37.55        66.05         7.36 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 
       67.50        91.99        82.85        49.58        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       97.48        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M 
       83.31         6.44        10.52        18.64        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 
       48.53         3.16        13.51        12.59        12.92         4.08 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO 
       11.34        11.28         0.16        10.42        12.95        12.33 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Z 
       12.36         8.28         9.67         9.50        24.56        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        18.90        12.03        53.00        14.01        18.97 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        19.40        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15        12.39        15.22        14.73        14.50        19.92 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.41        15.85        16.64        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-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        48.03        13.48         4.80         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 
       13.08        12.26        33.37        43.00        34.42        46.59 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.44        28.87        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       75.98        32.02        31.96        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
        9.04        20.58        50.79        19.56        56.94        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       53.62        87.22        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IO 
       37.41        70.36        33.70        28.44         3.88        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE 
       11.08        54.18        60.36        19.66        24.59        28.90 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        52.73        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
       34.92        34.82        36.82        36.20        36.56        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-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       32.05        41.03        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       38.99         1.94         7.13        24.56        12.33        29.72 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       38.07        32.91        30.44        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       25.81        26.40        18.21        18.90        13.25        16.57 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       28.77        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       13.94        10.52        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       25.91        22.09        10.16         7.40       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DK TCGA-GM-A2DM 
       79.10        83.34        75.02        70.85        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL 
      101.62        43.73        66.38        72.03        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-MS-A51U 
       62.47        11.84        32.75        14.70        14.79        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K 
       41.92 

$FC.NEUTRAL
TCGA-A1-A0SE TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y 
       43.43        13.68        18.21       121.94        63.12        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SW 
      136.73        99.12       114.81        24.72        99.19        44.88 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A3XZ 
       19.56        16.47        52.47        18.15        39.65        50.37 
TCGA-A2-A4RX TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A26J TCGA-A8-A06P TCGA-A8-A06T 
       24.39        37.45        29.79        20.61        13.02        53.06 
TCGA-A8-A07J TCGA-A8-A07U TCGA-A8-A08C TCGA-A8-A091 TCGA-AC-A2FE TCGA-AC-A2FF 
       12.00        24.99        28.96        33.01        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A3OD TCGA-AC-A3TM TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AN-A0AM 
       60.92        14.83        25.05        14.53        14.96         0.16 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03U TCGA-AO-A0JC 
        7.59         7.04        12.33         0.30        58.95        50.86 
TCGA-AO-A12A TCGA-AO-A12G TCGA-AR-A1AO TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A256 
       90.58        41.62        86.07        86.43       160.90        93.83 
TCGA-B6-A0RQ TCGA-B6-A0WW TCGA-B6-A1KF TCGA-BH-A0AU TCGA-BH-A0B8 TCGA-BH-A0BG 
      140.48        18.35       101.52        62.93        51.58        61.51 
TCGA-BH-A0BO TCGA-BH-A0DI TCGA-BH-A0DV TCGA-BH-A0H5 TCGA-BH-A0HF TCGA-BH-A0HN 
       72.23        29.98        67.86        53.26        23.90        16.96 
TCGA-BH-A18K TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1FM 
       90.84       113.82        42.28        55.69        17.69        45.63 
TCGA-BH-A42U TCGA-C8-A3M8 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XO TCGA-D8-A1XS 
      109.28        12.95        27.58        21.80        55.30        16.31 
TCGA-D8-A1XU TCGA-D8-A27L TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A10A TCGA-E2-A14N 
       12.99        16.41        18.51        21.67        40.41        47.15 
TCGA-E2-A14U TCGA-E2-A15S TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1IK TCGA-E2-A1L8 
       43.33        14.07        33.01        32.35        59.18        73.64 
TCGA-E2-A1LI TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RD 
      102.61        32.88        34.16        39.55        41.62         1.12 
TCGA-E9-A229 TCGA-E9-A22E TCGA-EW-A1P3 TCGA-GM-A3NY TCGA-GM-A5PV TCGA-LL-A440 
       37.74        41.72        52.96        38.20        13.55        24.95 
TCGA-LL-A50Y TCGA-LL-A5YM TCGA-OL-A5RY 
       25.05        15.32        24.72 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
         0.03          0.16          0.16 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       255.68        282.90        160.90 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       30.625        29.030        37.740 
[1] "0.0 - 255.7 (30.6)" "0.2 - 282.9 (29.0)" "0.2 - 160.9 (37.7)"
D2V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FC.HIGH.SIG        26       10        1        1        73        56
  FC.LOW.NONSIG      49       52        4        3       227       146
  FC.NEUTRAL         12       11        1        0        27        24
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS
  FC.HIGH.SIG           1         31          4         10        3         0
  FC.LOW.NONSIG         1         86         21         43       11         1
  FC.NEUTRAL            0         19          1          4        1         0
               vv
clus            STAGE X
  FC.HIGH.SIG         2
  FC.LOW.NONSIG       9
  FC.NEUTRAL          1
D2V3, multiclass
            clus
vv           FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  STAGE I             26            49         12
  STAGE IA            10            52         11
  STAGE IB             1             4          1
  STAGE II             1             3          0
  STAGE IIA           73           227         27
  STAGE IIB           56           146         24
  STAGE III            1             1          0
  STAGE IIIA          31            86         19
  STAGE IIIB           4            21          1
  STAGE IIIC          10            43          4
  STAGE IV             3            11          1
  STAGE TIS            0             1          0
  STAGE X              2             9          1
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FC.HIGH.SIG    49 130  33   7
  FC.LOW.NONSIG 178 379  71  27
  FC.NEUTRAL     31  54  15   1
D2V4, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  T1          49           178         31
  T2         130           379         54
  T3          33            71         15
  T4           7            27          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"
               vv
clus             N0  N1  N2  N3
  FC.HIGH.SIG   110  73  23  12
  FC.LOW.NONSIG 302 220  70  52
  FC.NEUTRAL     50  32  14   4
D2V5, multiclass
    clus
vv   FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  N0         110           302         50
  N1          73           220         32
  N2          23            70         14
  N3          12            52          4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
               cls
clus              0   1
  FC.HIGH.SIG   189   3
  FC.LOW.NONSIG 566  12
  FC.NEUTRAL     86   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    189    3
  FC.LOW.NONSIG  566   12
  FC.NEUTRAL      86    1
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0         189           566         86
  1           3            12          1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
               cls
clus              0   1
  FC.HIGH.SIG   218   2
  FC.LOW.NONSIG 650   6
  FC.NEUTRAL    100   1
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG    218    2
  FC.LOW.NONSIG  650    6
  FC.NEUTRAL     100    1
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE         218           650        100
  MALE             2             6          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"
D2V8, binary
               cls
clus              0   1
  FC.HIGH.SIG    88 100
  FC.LOW.NONSIG 250 323
  FC.NEUTRAL     39  49
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG     88  100
  FC.LOW.NONSIG  250  323
  FC.NEUTRAL      39   49
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO           88           250         39
  YES         100           323         49
[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.SIG                            0                           152
  FC.LOW.NONSIG                          1                           491
  FC.NEUTRAL                             0                            69
               vv
clus            INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  FC.HIGH.SIG                               54                   4
  FC.LOW.NONSIG                             95                   1
  FC.NEUTRAL                                22                   0
               vv
clus            METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  FC.HIGH.SIG                       1                                5
  FC.LOW.NONSIG                     4                               18
  FC.NEUTRAL                        1                                3
               vv
clus            MUCINOUS CARCINOMA OTHER  SPECIFY
  FC.HIGH.SIG                    0              3
  FC.LOW.NONSIG                 13             33
  FC.NEUTRAL                     1              5
D2V9, multiclass
                                  clus
vv                                 FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  INFILTRATING CARCINOMA NOS                 0             1          0
  INFILTRATING DUCTAL CARCINOMA            152           491         69
  INFILTRATING LOBULAR CARCINOMA            54            95         22
  MEDULLARY CARCINOMA                        4             1          0
  METAPLASTIC CARCINOMA                      1             4          1
  MIXED HISTOLOGY (PLEASE SPECIFY)           5            18          3
  MUCINOUS CARCINOMA                         0            13          1
  OTHER  SPECIFY                             3            33          5
[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.SIG                                  0    24
  FC.LOW.NONSIG                                1    31
  FC.NEUTRAL                                   0     2
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG                          35   138
  FC.LOW.NONSIG                        74   488
  FC.NEUTRAL                           12    79
D2V11, multiclass
                                  clus
vv                                 FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  AMERICAN INDIAN OR ALASKA NATIVE           0             1          0
  ASIAN                                     24            31          2
  BLACK OR AFRICAN AMERICAN                 35            74         12
  WHITE                                    138           488         79
[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.SIG     6 175
  FC.LOW.NONSIG  28 512
  FC.NEUTRAL      0  85
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      6  175
  FC.LOW.NONSIG   28  512
  FC.NEUTRAL       0   85
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               6            28          0
  NOT HISPANIC OR LATINO         175           512         85
[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"
