[1] "ofn"        "-oTSKCM-TM"
[1] "opt"       "-OPAPOBEC"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "APOBEC"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/22507034/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/SKCM-TM/22541894/__DELETED__1436046:APOBEC_clinical_corr_input_22563710/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=368, in cluster file=290, common to both=290
[1]   2 290
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
  86   99  105 
   0 HIGH  LOW 
  86   99  105 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             3            201             86 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             3            201             86 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "DAYS_TO_SUBMITTED_SPECIMEN_DX"       
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "MELANOMA_ULCERATION"                 
[11] "MELANOMA_PRIMARY_KNOWN"              
[12] "BRESLOW_THICKNESS"                   
[13] "GENDER"                              
[14] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[15] "RADIATION_THERAPY"                   
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 290 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=66,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=158,	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=122,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DAYS_TO_SUBMITTED_SPECIMEN_DX':	nDistinctValues=231,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MELANOMA_ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA_PRIMARY_KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BRESLOW_THICKNESS':	nDistinctValues=99,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 15:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	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] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "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 290 columns, 2 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP"
[2] "VITAL_STATUS"                              
[3] "DAYS_TO_DEATH_OR_LAST_FUP"                 
[4] "VITAL_STATUS"                              
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"         "PATHOLOGIC_STAGE"       "PATHOLOGY_T_STAGE"     
 [4] "PATHOLOGY_N_STAGE"      "PATHOLOGY_M_STAGE"      "MELANOMA_ULCERATION"   
 [7] "MELANOMA_PRIMARY_KNOWN" "BRESLOW_THICKNESS"      "GENDER"                
[10] "RADIATION_THERAPY"      "RACE"                   "ETHNICITY"             
YEARS_TO_BIRTH, nv=66, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
23 30 62 60 55 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53    62    60    55 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 30 62 60 55 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53    62    60    55 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
143  53  34  35 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
143  53  34  35 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
143  53  34  35 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
143  53  34  35 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
MELANOMA_ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA_PRIMARY_KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW_THICKNESS, nv=99, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2   0  1
  0    21 35
  HIGH 38 32
  LOW  38 36
   0 HIGH  LOW 
  56   70   74 
   0 HIGH  LOW 
  35   32   36 
$`0`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JB 
        8.42        15.72       110.93       133.25        25.64       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       86.30       107.61        58.06        59.70        24.53         9.34 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY 
      173.85        30.67        31.76        22.29        22.85       138.67 
TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A29P 
       30.44         3.91        16.41        52.41        18.21        27.16 
TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MP 
      185.19        10.62        71.31        15.25        94.19       227.01 
TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L 
       67.89        10.49         7.82        53.29       184.60        99.06 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      120.76        49.71        47.18        73.05         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       10.19       173.29        68.52       171.78        49.74        27.62 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        7.82        36.33        78.61        35.28         4.47         5.29 
TCGA-GN-A265 TCGA-RP-A690 
       96.92         0.20 

$HIGH
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD 
       62.07        38.76       269.03        52.90       134.40        27.35 
TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A1QA TCGA-D3-A2J8 TCGA-D3-A2JH 
       19.04        36.85        49.35        76.41        62.86        36.30 
TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51R TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HV 
       90.21        23.67        62.70        11.34        69.21        76.34 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 
       60.10        64.83        58.85        42.64        13.15        20.38 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D 
        0.00        26.24        75.55        79.20        75.22        12.99 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GM 
        0.26        47.74        30.02        26.14        68.65        18.35 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ 
       93.63         0.20        81.99       209.79       171.85        63.25 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
      143.93        23.51        53.26       124.31        64.04        54.51 
TCGA-EE-A3AF TCGA-EE-A3J7 TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19A TCGA-ER-A19N 
        6.28        45.90       168.85       135.98         4.54        42.51 
TCGA-ER-A19W TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZQ TCGA-FS-A1ZW 
      146.63        74.47         8.35       312.07       130.95        23.21 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A267 
        3.06        80.68        55.59        11.54         9.90        17.06 
TCGA-GN-A4U4 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
       34.49       297.01         7.23         0.33 

$LOW
TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1QB 
       33.24        31.96       166.75        31.89        19.04        62.60 
TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       45.99        15.75       171.58        64.83        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
      140.98        40.01       144.46        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A17Y 
       15.02        68.68       150.61       110.53       225.11        24.89 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 
       76.14        44.28        47.41        61.12       346.49       115.43 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M6 
       77.98        12.95       201.60        32.48         0.76       103.13 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AB 
        5.75        23.77        89.26       104.78       145.45       122.73 
TCGA-EE-A3AD TCGA-EE-A3J4 TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19C 
        4.41       111.85         3.35        19.86        34.45        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3EV 
       11.47       150.12        59.84        22.36        28.67        15.48 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1ZD TCGA-FS-A1ZE 
       32.05         4.50       174.21       195.98        32.78        43.92 
TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A5DY 
      136.27        18.51        66.67       173.19        13.28        19.30 
TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A 
       18.25         1.91        53.29       117.93        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 
      120.53        46.92 

   0 HIGH  LOW 
0.20 0.00 0.76 
     0   HIGH    LOW 
227.01 312.07 346.49 
     0   HIGH    LOW 
41.755 53.080 45.845 
[1] "0.2 - 227.0 (41.8)" "0.0 - 312.1 (53.1)" "0.8 - 346.5 (45.8)"
D1V2, survival
      sevent
clus2   0  1
  0    31 53
  HIGH 48 48
  LOW  45 59
   0 HIGH  LOW 
  84   96  104 
   0 HIGH  LOW 
  53   48   59 
$`0`
TCGA-EB-A5SH TCGA-EE-A184 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       54.02        68.15        16.57        16.67       112.57       133.25 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       31.59        43.43        23.77       168.00        86.76       113.52 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E 
      130.72        58.06        60.23        24.53         9.34       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A149 TCGA-D9-A3Z3 
       55.73        56.35        32.94        22.62        54.67        22.29 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 
       22.95       144.89        20.38        35.93        40.60        33.93 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        20.35        58.92         7.04        36.46 
TCGA-EE-A17Z TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GK 
        8.65       133.81        13.55        56.42       195.02        54.74 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       81.21        44.88        28.83       103.27       103.20        16.96 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
      248.65       172.18        13.94         9.17        98.40       302.07 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
      131.51       162.08        50.89        49.48         8.88       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A69P 
       23.34        20.15        28.83       247.04        93.01        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZH 
      216.92        48.59       228.59        28.08         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38       101.26        11.41        53.16        26.56        27.09 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-RP-A690 
       26.73        17.46        96.92        48.00        22.13         0.20 

$HIGH
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO 
       62.07        46.32        13.87         2.60       340.14       126.81 
TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q6 TCGA-D3-A1QA 
      134.40        27.35        31.40        36.95        71.80        90.90 
TCGA-D3-A2J8 TCGA-D3-A2JH TCGA-D3-A3C7 TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       65.49        42.08        46.98       103.59        39.75        45.30 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU TCGA-D9-A6EA TCGA-D9-A6EC 
       63.81        26.89       137.92       125.19        25.18        77.56 
TCGA-DA-A1HV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X 
       76.57        88.87        65.92        68.09        43.36        29.82 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B 
       33.73        14.70        26.89       151.27        91.56        85.08 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       13.97        63.78        56.84        18.61        14.47        61.28 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
       25.87        59.64        59.28        67.43        48.72       107.38 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2MD 
       75.48       102.12        42.77        94.82        21.67        47.28 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      268.73       204.66        96.23       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J5 
      124.31        64.04        54.51        13.81        41.59        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JI TCGA-ER-A19A TCGA-ER-A19F 
       64.08        53.19       201.80       152.81        77.75        26.37 
TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       44.09       148.18       149.03        20.91        27.72       357.37 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4FC 
       23.93        74.73       133.55        49.48        27.02        54.41 
TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GF-A6C9 TCGA-GN-A266 
       80.68        55.59        13.51         9.90        15.78        10.13 
TCGA-GN-A267 TCGA-GN-A4U4 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       64.44        39.35       297.90         7.23         0.33         0.69 

$LOW
TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-ER-A198 TCGA-FS-A1ZF TCGA-D3-A1Q4 
       68.25        94.98       168.26        50.76        15.45       112.04 
TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JK 
       28.08        95.74       103.10       115.53        11.87        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC 
      171.58        66.48        66.08        59.57       166.52        86.93 
TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 
      145.12       125.79       135.75       178.32        18.18       151.53 
TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I1 
        3.65         7.10        15.39         9.90        36.03       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5UL 
      176.55       135.02        53.92        10.49       225.96        29.29 
TCGA-EE-A17Y TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H 
       27.22         4.96        63.35        78.97        72.07        64.64 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
       66.74       369.93        17.92        46.82       115.96        39.29 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2M6 
       86.14       173.79       220.24        79.66        13.91       129.27 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
       19.76        61.51       180.39       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J8 
       43.23       122.73        28.77       138.81       127.20        34.32 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       51.35       134.33        35.44        48.89        12.59        13.02 
TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH 
      152.35         6.44        61.05        43.82        48.99        41.56 
TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z0 
       46.98        33.21        12.95        92.98       174.21       202.65 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZS TCGA-FS-A4F0 
        7.79        48.85        53.52        46.45       148.80        77.82 
TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A5DY TCGA-GF-A4EO 
       66.67        28.73       174.84        34.03        19.30        19.43 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
        2.04       139.89       117.93        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U8 
       10.42        48.89 

   0 HIGH  LOW 
0.20 0.33 2.04 
     0   HIGH    LOW 
302.07 357.37 369.93 
     0   HIGH    LOW 
46.130 56.215 62.150 
[1] "0.2 - 302.1 (46.1)" "0.3 - 357.4 (56.2)" "2.0 - 369.9 (62.1)"
D1V3, continuous
      vv
clus   I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  0           3       3       7        0        6        3         2         4
  HIGH        4       3       6        7        7        9         5         6
  LOW         3       0      12        3       12        6         3         4
      vv
clus   STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  0            5        10          3          9         15        6
  HIGH         1        11          4         12         13        5
  LOW          4        15          7          5         15        5
D1V4, multiclass
            clus
vv            0 HIGH LOW
  I/II NOS    3    4   3
  STAGE 0     3    3   0
  STAGE I     7    6  12
  STAGE IA    0    7   3
  STAGE IB    6    7  12
  STAGE II    3    9   6
  STAGE IIA   2    5   3
  STAGE IIB   4    6   4
  STAGE IIC   5    1   4
  STAGE III  10   11  15
  STAGE IIIA  3    4   7
  STAGE IIIB  9   12   5
  STAGE IIIC 15   13  15
  STAGE IV    6    5   5
[1] 14  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   T0+T1 T2 T3 T4
  0       11 17 14 20
  HIGH    20 19 23 16
  LOW     22 26 23 19
D1V5, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 11   20  22
  T2    17   19  26
  T3    14   23  23
  T4    20   16  19
[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    40 14 11 15
  HIGH 51 17 14  7
  LOW  52 22  9 13
D1V6, multiclass
    clus
vv    0 HIGH LOW
  N0 40   51  52
  N1 14   17  22
  N2 11   14   9
  N3 15    7  13
[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"
D1V7, binary
      cls
clus    0  1
  0    73  6
  HIGH 89  5
  LOW  94  6
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      73    6
  HIGH   89    5
  LOW    94    6
   clus
vv   0 HIGH LOW
  0 73   89  94
  1  6    5   6
[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    23 28
  HIGH 36 20
  LOW  48 25
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23   28
  HIGH   36   20
  LOW    48   25
     clus
vv     0 HIGH LOW
  NO  23   36  48
  YES 28   20  25
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
      cls
clus    0  1
  0     9 77
  HIGH 17 82
  LOW  11 94
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       9   77
  HIGH   17   82
  LOW    11   94
     clus
vv     0 HIGH LOW
  NO   9   17  11
  YES 77   82  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"
D1V10, continuous
D1V11, binary
      cls
clus    0  1
  0    40 46
  HIGH 27 72
  LOW  42 63
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      40   46
  HIGH   27   72
  LOW    42   63
        clus
vv        0 HIGH LOW
  FEMALE 40   27  42
  MALE   46   72  63
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
      cls
clus    0  1
  0    75 10
  HIGH 85 14
  LOW  94 11
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      75   10
  HIGH   85   14
  LOW    94   11
     clus
vv     0 HIGH LOW
  NO  75   85  94
  YES 10   14  11
[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   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  0        4                         1    81
  HIGH     0                         0    99
  LOW      1                         0   104
D1V13, multiclass
                           clus
vv                            0 HIGH LOW
  ASIAN                       4    0   1
  BLACK OR AFRICAN AMERICAN   1    0   0
  WHITE                      81   99 104
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
      cls
clus     0   1
  0      2  84
  HIGH   1  97
  LOW    0 102
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       2   84
  HIGH    1   97
  LOW     0  102
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       2    1   0
  NOT HISPANIC OR LATINO  84   97 102
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2             0  1
  FC.HIGH.ENRICH  1  2
  FC.LOW.ENRICH  75 66
  FC.NO.ENRICH   21 35
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             3            141             56 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             2             66             35 
$FC.HIGH.ENRICH
TCGA-D3-A3CC TCGA-FS-A4F4 TCGA-GN-A264 
       40.01        66.67       117.93 

$FC.LOW.ENRICH
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A2GD 
       62.07        38.76        33.24        31.96       166.75       269.03 
TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 TCGA-FW-A3R5 TCGA-D3-A1Q4 
       52.90       134.40        27.35        19.04        36.85        31.89 
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       49.35        19.04        76.41        62.60        45.99        62.86 
TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       15.75        36.30       171.58        64.83        66.08        43.53 
TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51R TCGA-D3-A51T 
      140.98        90.21        23.67       144.46        62.70        11.34 
TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV 
       42.05        45.70       177.86        15.02        69.21        76.34 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       68.68       150.61       110.53        60.10        64.83        58.85 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A181 TCGA-EE-A182 
      225.11        42.64        13.15        24.89        20.38         0.00 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
       26.24        75.55        79.20        75.22        76.14        12.99 
TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29T 
        0.26        44.28        47.41        47.74        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
      115.43        30.02        77.98        26.14        12.95       201.60 
TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GR 
       68.65        32.48        18.35        93.63         0.76         0.20 
TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI 
       81.99       103.13         5.75        23.77       209.79       171.85 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MS TCGA-EE-A2MT 
       63.25        89.26       104.78       145.45       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
       53.26       124.31       122.73        64.04         4.41        54.51 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH 
        6.28       111.85        45.90         3.35       168.85        19.86 
TCGA-EE-A3JI TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
      135.98        34.45         4.54        39.81        11.47       150.12 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3EV 
       59.84        42.51       146.63        22.36        28.67        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       32.05        74.47         4.50       174.21       195.98         8.35 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
      312.07        32.78        43.92       130.95       136.27        23.21 
TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FD TCGA-FW-A3TU 
        3.06        18.51       173.19        13.28        80.68        55.59 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
       11.54        19.30         9.90        18.25         1.91        53.29 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U8 
       17.06        42.48         7.59       120.53        34.49        46.92 
TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 
      297.01         7.23         0.33 

$FC.NO.ENRICH
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2JB 
        8.42        15.72       110.93       133.25        25.64       168.00 
TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       86.30       107.61        58.06        59.70        24.53         9.34 
TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51K TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY 
      173.85        30.67        31.76        22.29        22.85       138.67 
TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A29P 
       30.44         3.91        16.41        52.41        18.21        27.16 
TCGA-EE-A29W TCGA-EE-A2GK TCGA-EE-A2GS TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MP 
      185.19        10.62        71.31        15.25        94.19       227.01 
TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L 
       67.89        10.49         7.82        53.29       184.60        99.06 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE 
      120.76        49.71        47.18        73.05         4.70        16.87 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 
       10.19       173.29        68.52       171.78        49.74        27.62 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
        7.82        36.33        78.61        35.28         4.47         5.29 
TCGA-GN-A265 TCGA-RP-A690 
       96.92         0.20 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         40.01           0.00           0.20 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        117.93         346.49         227.01 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        66.670         47.410         41.755 
[1] "40.0 - 117.9 (66.7)" "0.0 - 346.5 (47.4)"  "0.2 - 227.0 (41.8)" 
D2V2, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH   1   2
  FC.LOW.ENRICH   92 105
  FC.NO.ENRICH    31  53
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             3            197             84 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             2            105             53 
$FC.HIGH.ENRICH
TCGA-D3-A3CC TCGA-FS-A4F4 TCGA-GN-A264 
       86.93        66.67       117.93 

$FC.LOW.ENRICH
TCGA-D3-A2JF TCGA-D3-A3C8 TCGA-D3-A3ML TCGA-EB-A5SG TCGA-EE-A180 TCGA-EE-A20H 
       62.07        46.32        13.87        68.25        94.98       168.26 
TCGA-EE-A29L TCGA-EE-A2GD TCGA-EE-A2GO TCGA-EE-A2MR TCGA-EE-A3JD TCGA-ER-A193 
        2.60       340.14       126.81       134.40        27.35        31.40 
TCGA-ER-A198 TCGA-FS-A1ZF TCGA-FW-A3R5 TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 
       50.76        15.45        36.95       112.04        71.80        28.08 
TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JD 
       90.90        95.74       103.10        65.49       115.53        11.87 
TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP 
       42.08        12.10       171.58        66.48        66.08        59.57 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51J 
       46.98       166.52       103.59        39.75        45.30       145.12 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
       63.81        26.89       125.79       135.75       137.92       178.32 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 
       18.18       125.19       151.53         3.65         7.10        15.39 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 
        9.90        25.18        77.56        76.57        36.03       222.51 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
      176.55       135.02        88.87        53.92        65.92        68.09 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y 
       10.49       225.96        43.36        29.29        29.82        27.22 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F 
       33.73        14.70        26.89         4.96       151.27        91.56 
TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G 
       63.35        85.08        78.97        13.97        63.78        72.07 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       64.64        56.84        18.61        66.74        14.47        61.28 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
      369.93        25.87        17.92        46.82       115.96        59.64 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH 
       39.29        86.14        59.28        67.43       173.79       220.24 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
       48.72       107.38        79.66        75.48       102.12        13.91 
TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC 
       42.77        94.82        21.67       129.27        19.76        61.51 
TCGA-EE-A2MD TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       47.28       268.73       204.66        96.23       180.39       216.66 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
      167.90        47.54        43.23       162.48        71.21        53.26 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
      124.31       122.73        64.04        28.77        54.51        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 
       41.59       138.81       127.20        36.95        64.08        34.32 
TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A195 
       53.19       201.80        51.35       134.33       152.81        35.44 
TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19H 
       77.75        48.89        12.59        13.02        26.37       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG 
        6.44        61.05        44.09       148.18        43.82        48.99 
TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K TCGA-ER-A42L TCGA-FR-A3YN 
       41.56        46.98        33.21        12.95       149.03        92.98 
TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
      174.21       202.65        20.91         7.79        27.72        48.85 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ 
      357.37        53.52        46.45        23.93        74.73       133.55 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 
      148.80        49.48        27.02        77.82        28.73       174.84 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY 
       34.03        54.41        80.68        55.59        13.51        19.30 
TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 
        9.90        19.43         2.04        15.78       139.89        10.13 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 
       64.44        62.79        32.48       121.91        39.35        10.42 
TCGA-GN-A4U8 TCGA-OD-A75X TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
       48.89       297.90         7.23         0.33         0.69 

$FC.NO.ENRICH
TCGA-EB-A5SH TCGA-EE-A184 TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 
       54.02        68.15        16.57        16.67       112.57       133.25 
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG 
       31.59        43.43        23.77       168.00        86.76       113.52 
TCGA-D3-A3BZ TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E 
      130.72        58.06        60.23        24.53         9.34       174.84 
TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A149 TCGA-D9-A3Z3 
       55.73        56.35        32.94        22.62        54.67        22.29 
TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 
       22.95       144.89        20.38        35.93        40.60        33.93 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       13.87        10.36        20.35        58.92         7.04        36.46 
TCGA-EE-A17Z TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GK 
        8.65       133.81        13.55        56.42       195.02        54.74 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       81.21        44.88        28.83       103.27       103.20        16.96 
TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G 
      248.65       172.18        13.94         9.17        98.40       302.07 
TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19T TCGA-ER-A1A1 
      131.51       162.08        50.89        49.48         8.88       105.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A69P 
       23.34        20.15        28.83       247.04        93.01        15.72 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZH 
      216.92        48.59       228.59        28.08         9.70        32.75 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY 
       47.38       101.26        11.41        53.16        26.56        27.09 
TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U9 TCGA-RP-A690 
       26.73        17.46        96.92        48.00        22.13         0.20 

FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         66.67           0.33           0.20 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
        117.93         369.93         302.07 
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
         86.93          59.28          46.13 
[1] "66.7 - 117.9 (86.9)" "0.3 - 369.9 (59.3)"  "0.2 - 302.1 (46.1)" 
D2V3, continuous
                vv
clus             I/II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  FC.HIGH.ENRICH        0       0       0        0        0        1         0
  FC.LOW.ENRICH         7       3      18       10       19       14         8
  FC.NO.ENRICH          3       3       7        0        6        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FC.HIGH.ENRICH         0         1         0          0          0          0
  FC.LOW.ENRICH         10         4        26         11         17         28
  FC.NO.ENRICH           4         5        10          3          9         15
                vv
clus             STAGE IV
  FC.HIGH.ENRICH        0
  FC.LOW.ENRICH        10
  FC.NO.ENRICH          6
D2V4, multiclass
[1] "Remove cluster labels:" "FC.HIGH.ENRICH"        
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             2            185             76 
   TCGA-D3-A2JF    TCGA-D3-A3C8    TCGA-D3-A3ML    TCGA-D3-A51G    TCGA-EB-A5SH 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A180    TCGA-EE-A184    TCGA-EE-A20H    TCGA-EE-A29L    TCGA-EE-A2GD 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GO    TCGA-EE-A2MR    TCGA-EE-A3JD    TCGA-ER-A193    TCGA-FR-A3YO 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZF    TCGA-FW-A3R5    TCGA-D3-A1Q1    TCGA-D3-A1Q3    TCGA-D3-A1Q4 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A1Q5    TCGA-D3-A1Q6    TCGA-D3-A1Q7    TCGA-D3-A1Q8    TCGA-D3-A1Q9 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A1QA    TCGA-D3-A1QB    TCGA-D3-A2J6    TCGA-D3-A2J7    TCGA-D3-A2J8 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2J9    TCGA-D3-A2JA    TCGA-D3-A2JB    TCGA-D3-A2JC    TCGA-D3-A2JD 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2JG    TCGA-D3-A2JH    TCGA-D3-A2JK    TCGA-D3-A2JL    TCGA-D3-A2JN 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2JO    TCGA-D3-A2JP    TCGA-D3-A3BZ    TCGA-D3-A3C1    TCGA-D3-A3C3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A3C6    TCGA-D3-A3C7    TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A3MO    TCGA-D3-A3MR    TCGA-D3-A3MU    TCGA-D3-A3MV    TCGA-D3-A51E 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A51F    TCGA-D3-A51H    TCGA-D3-A51J    TCGA-D3-A51K    TCGA-D3-A51N 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A51R    TCGA-D3-A51T    TCGA-D3-A5GL    TCGA-D3-A5GN    TCGA-D3-A5GO 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A5GR    TCGA-D3-A5GS    TCGA-D3-A5GU    TCGA-D9-A3Z1    TCGA-D9-A3Z3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D9-A6E9    TCGA-D9-A6EA    TCGA-D9-A6EC    TCGA-D9-A6EG    TCGA-DA-A1HV 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A1HW    TCGA-DA-A1HY    TCGA-DA-A1I0    TCGA-DA-A1I1    TCGA-DA-A1I2 
"FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A1I4    TCGA-DA-A1I5    TCGA-DA-A1I7    TCGA-DA-A1I8    TCGA-DA-A1IA 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A1IB    TCGA-DA-A1IC    TCGA-DA-A3F2    TCGA-DA-A3F3    TCGA-DA-A3F5 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A3F8    TCGA-EB-A44Q    TCGA-EB-A44R    TCGA-EB-A5KH    TCGA-EB-A5UL 
"FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EB-A5UN    TCGA-EB-A5VV    TCGA-EB-A6L9    TCGA-EE-A17X    TCGA-EE-A17Y 
 "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A17Z    TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A183    TCGA-EE-A185 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A20B    TCGA-EE-A20C    TCGA-EE-A20F    TCGA-EE-A20I    TCGA-EE-A29A 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29B    TCGA-EE-A29C    TCGA-EE-A29D    TCGA-EE-A29E    TCGA-EE-A29G 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29H    TCGA-EE-A29M    TCGA-EE-A29N    TCGA-EE-A29P    TCGA-EE-A29Q 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29R    TCGA-EE-A29S    TCGA-EE-A29V    TCGA-EE-A29W    TCGA-EE-A29X 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2A0    TCGA-EE-A2A1    TCGA-EE-A2A2    TCGA-EE-A2A5    TCGA-EE-A2A6 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GB    TCGA-EE-A2GC    TCGA-EE-A2GE    TCGA-EE-A2GH    TCGA-EE-A2GI 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GJ    TCGA-EE-A2GK    TCGA-EE-A2GL    TCGA-EE-A2GM    TCGA-EE-A2GN 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GP    TCGA-EE-A2GR    TCGA-EE-A2GS    TCGA-EE-A2GT    TCGA-EE-A2GU 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2M5    TCGA-EE-A2M6    TCGA-EE-A2M7    TCGA-EE-A2M8    TCGA-EE-A2MC 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MD    TCGA-EE-A2ME    TCGA-EE-A2MF    TCGA-EE-A2MG    TCGA-EE-A2MH 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A2MI    TCGA-EE-A2MJ    TCGA-EE-A2MK    TCGA-EE-A2ML    TCGA-EE-A2MM 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MN    TCGA-EE-A2MP    TCGA-EE-A2MQ    TCGA-EE-A2MS    TCGA-EE-A2MT 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB    TCGA-EE-A3AC    TCGA-EE-A3AD 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG    TCGA-EE-A3AH    TCGA-EE-A3J3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7    TCGA-EE-A3J8    TCGA-EE-A3JA 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3JB    TCGA-EE-A3JE    TCGA-EE-A3JH    TCGA-EE-A3JI    TCGA-ER-A197 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A199    TCGA-ER-A19A    TCGA-ER-A19C    TCGA-ER-A19D    TCGA-ER-A19E 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A19J    TCGA-ER-A19M    TCGA-ER-A19O    TCGA-ER-A19T    TCGA-ER-A1A1 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A2NC    TCGA-ER-A2ND    TCGA-ER-A2NE    TCGA-ER-A2NF    TCGA-ER-A2NG 
"FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A2NH    TCGA-ER-A3ET    TCGA-ER-A3EV    TCGA-ER-A3PL    TCGA-ER-A42K 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A42L    TCGA-FR-A3YN    TCGA-FR-A44A    TCGA-FR-A69P    TCGA-FS-A1YW 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1YX    TCGA-FS-A1YY    TCGA-FS-A1Z0    TCGA-FS-A1Z3    TCGA-FS-A1Z4 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1Z7    TCGA-FS-A1ZA    TCGA-FS-A1ZB    TCGA-FS-A1ZC    TCGA-FS-A1ZD 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZE    TCGA-FS-A1ZG    TCGA-FS-A1ZH    TCGA-FS-A1ZJ    TCGA-FS-A1ZK 
"FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZM    TCGA-FS-A1ZP    TCGA-FS-A1ZQ    TCGA-FS-A1ZR    TCGA-FS-A1ZS 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZT    TCGA-FS-A1ZU    TCGA-FS-A1ZW    TCGA-FS-A1ZY    TCGA-FS-A1ZZ 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A4F0    TCGA-FS-A4F5    TCGA-FS-A4F8    TCGA-FS-A4F9    TCGA-FS-A4FB 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A4FC    TCGA-FS-A4FD    TCGA-FW-A3I3    TCGA-FW-A3TV    TCGA-FW-A5DY 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GF-A3OT    TCGA-GF-A4EO    TCGA-GF-A6C8    TCGA-GF-A6C9    TCGA-GN-A267 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3    TCGA-GN-A4U4 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS    TCGA-RP-A693    TCGA-RP-A694 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-RP-A695 
"FC.LOW.ENRICH" 
            clus
vv           FC.LOW.ENRICH FC.NO.ENRICH
  I/II NOS               7            3
  STAGE 0                3            3
  STAGE I               18            7
  STAGE IA              10            0
  STAGE IB              19            6
  STAGE II              14            3
  STAGE IIA              8            2
  STAGE IIB             10            4
  STAGE IIC              4            5
  STAGE III             26           10
  STAGE IIIA            11            3
  STAGE IIIB            17            9
  STAGE IIIC            28           15
  STAGE IV              10            6
[1] 14  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1 T2 T3 T4
  FC.HIGH.ENRICH     0  0  1  1
  FC.LOW.ENRICH     42 45 45 34
  FC.NO.ENRICH      11 17 14 20
D2V5, multiclass
[1] "Remove cluster labels:" "FC.HIGH.ENRICH"        
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             2            166             62 
   TCGA-D3-A2JF    TCGA-D3-A3ML    TCGA-EB-A5SH    TCGA-EE-A180    TCGA-EE-A184 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A20H    TCGA-EE-A29L    TCGA-EE-A2GD    TCGA-EE-A2GO    TCGA-EE-A2MR 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A193    TCGA-FR-A3YO    TCGA-FS-A1ZF    TCGA-D3-A1Q1    TCGA-D3-A1Q3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A1Q4    TCGA-D3-A1Q6    TCGA-D3-A1Q7    TCGA-D3-A1Q8    TCGA-D3-A1Q9 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A1QA    TCGA-D3-A1QB    TCGA-D3-A2J6    TCGA-D3-A2J7    TCGA-D3-A2J8 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2J9    TCGA-D3-A2JA    TCGA-D3-A2JC    TCGA-D3-A2JD    TCGA-D3-A2JG 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A2JH    TCGA-D3-A2JK    TCGA-D3-A2JN    TCGA-D3-A2JP    TCGA-D3-A3BZ 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A3C6    TCGA-D3-A3C7    TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A3MR    TCGA-D3-A3MU    TCGA-D3-A3MV    TCGA-D3-A51E    TCGA-D3-A51F 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A51H    TCGA-D3-A51J    TCGA-D3-A51N    TCGA-D3-A51R    TCGA-D3-A51T 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A5GL    TCGA-D3-A5GN    TCGA-D3-A5GO    TCGA-D3-A5GR    TCGA-D3-A5GS 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A5GU    TCGA-D9-A1JW    TCGA-D9-A3Z1    TCGA-D9-A3Z3    TCGA-D9-A6E9 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D9-A6EA    TCGA-D9-A6EC    TCGA-D9-A6EG    TCGA-DA-A1HV    TCGA-DA-A1HW 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A1HY    TCGA-DA-A1I0    TCGA-DA-A1I1    TCGA-DA-A1I2    TCGA-DA-A1I4 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-DA-A1I5    TCGA-DA-A1I7    TCGA-DA-A1I8    TCGA-DA-A1IA    TCGA-DA-A1IB 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-DA-A1IC    TCGA-DA-A3F2    TCGA-DA-A3F3    TCGA-DA-A3F5    TCGA-DA-A3F8 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EB-A5KH    TCGA-EB-A5UN    TCGA-EB-A5VV    TCGA-EE-A17X    TCGA-EE-A17Y 
 "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A17Z    TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A185    TCGA-EE-A20B 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A20F    TCGA-EE-A29A    TCGA-EE-A29B    TCGA-EE-A29C    TCGA-EE-A29D 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29E    TCGA-EE-A29G    TCGA-EE-A29H    TCGA-EE-A29M    TCGA-EE-A29P 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A29Q    TCGA-EE-A29R    TCGA-EE-A29S    TCGA-EE-A29V    TCGA-EE-A29X 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2A0    TCGA-EE-A2A1    TCGA-EE-A2A2    TCGA-EE-A2A5    TCGA-EE-A2A6 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GB    TCGA-EE-A2GC    TCGA-EE-A2GE    TCGA-EE-A2GH    TCGA-EE-A2GI 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GJ    TCGA-EE-A2GK    TCGA-EE-A2GL    TCGA-EE-A2GM    TCGA-EE-A2GN 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GP    TCGA-EE-A2GR    TCGA-EE-A2GS    TCGA-EE-A2GT    TCGA-EE-A2GU 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2M5    TCGA-EE-A2M6    TCGA-EE-A2M7    TCGA-EE-A2M8    TCGA-EE-A2MC 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MD    TCGA-EE-A2ME    TCGA-EE-A2MF    TCGA-EE-A2MG    TCGA-EE-A2MH 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A2MI    TCGA-EE-A2MJ    TCGA-EE-A2MK    TCGA-EE-A2ML    TCGA-EE-A2MM 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MN    TCGA-EE-A2MP    TCGA-EE-A2MQ    TCGA-EE-A2MS    TCGA-EE-A2MT 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB    TCGA-EE-A3AC    TCGA-EE-A3AD 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG    TCGA-EE-A3AH    TCGA-EE-A3J3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7    TCGA-EE-A3J8    TCGA-EE-A3JA 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3JB    TCGA-EE-A3JE    TCGA-EE-A3JH    TCGA-EE-A3JI    TCGA-ER-A197 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A199    TCGA-ER-A19C    TCGA-ER-A19D    TCGA-ER-A19E    TCGA-ER-A19M 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A19O    TCGA-ER-A19T    TCGA-ER-A2NC    TCGA-ER-A2ND    TCGA-ER-A2NF 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A2NG    TCGA-ER-A2NH    TCGA-ER-A3ET    TCGA-ER-A3EV    TCGA-ER-A3PL 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A42K    TCGA-ER-A42L    TCGA-FR-A3YN    TCGA-FR-A44A    TCGA-FS-A1YW 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1YX    TCGA-FS-A1YY    TCGA-FS-A1Z0    TCGA-FS-A1Z4    TCGA-FS-A1Z7 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZA    TCGA-FS-A1ZB    TCGA-FS-A1ZD    TCGA-FS-A1ZE    TCGA-FS-A1ZG 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1ZH    TCGA-FS-A1ZJ    TCGA-FS-A1ZK    TCGA-FS-A1ZM    TCGA-FS-A1ZP 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZR    TCGA-FS-A1ZS    TCGA-FS-A1ZT    TCGA-FS-A1ZU    TCGA-FS-A1ZW 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZY    TCGA-FS-A1ZZ    TCGA-FS-A4F0    TCGA-FS-A4F5    TCGA-FS-A4F8 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A4F9    TCGA-FS-A4FB    TCGA-FS-A4FC    TCGA-FS-A4FD    TCGA-FW-A3TV 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FW-A5DY    TCGA-GF-A3OT    TCGA-GF-A4EO    TCGA-GF-A6C8    TCGA-GN-A267 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3    TCGA-GN-A4U4 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
       clus
vv      FC.LOW.ENRICH FC.NO.ENRICH
  T0+T1            42           11
  T2               45           17
  T3               45           14
  T4               34           20
[1] 4 2
[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   2   0   0   0
  FC.LOW.ENRICH  101  39  23  20
  FC.NO.ENRICH    40  14  11  15
D2V6, multiclass
[1] "Remove cluster labels:" "FC.HIGH.ENRICH"        
clus
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
             2            183             80 
   TCGA-D3-A2JF    TCGA-D3-A3C8    TCGA-D3-A3ML    TCGA-D3-A51G    TCGA-EB-A5SH 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A180    TCGA-EE-A184    TCGA-EE-A20H    TCGA-EE-A29L    TCGA-EE-A2GD 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GO    TCGA-EE-A2MR    TCGA-EE-A3JD    TCGA-ER-A193    TCGA-FR-A3YO 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZF    TCGA-FW-A3R5    TCGA-D3-A1Q1    TCGA-D3-A1Q3    TCGA-D3-A1Q4 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A1Q5    TCGA-D3-A1Q6    TCGA-D3-A1Q7    TCGA-D3-A1Q8    TCGA-D3-A1Q9 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A1QA    TCGA-D3-A1QB    TCGA-D3-A2J6    TCGA-D3-A2J7    TCGA-D3-A2J8 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2J9    TCGA-D3-A2JA    TCGA-D3-A2JB    TCGA-D3-A2JC    TCGA-D3-A2JD 
 "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2JG    TCGA-D3-A2JH    TCGA-D3-A2JK    TCGA-D3-A2JL    TCGA-D3-A2JN 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A2JO    TCGA-D3-A2JP    TCGA-D3-A3BZ    TCGA-D3-A3C1    TCGA-D3-A3C3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A3C6    TCGA-D3-A3C7    TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A3MO    TCGA-D3-A3MR    TCGA-D3-A3MU    TCGA-D3-A3MV    TCGA-D3-A51E 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A51F    TCGA-D3-A51H    TCGA-D3-A51J    TCGA-D3-A51K    TCGA-D3-A51N 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D3-A51R    TCGA-D3-A51T    TCGA-D3-A5GL    TCGA-D3-A5GN    TCGA-D3-A5GO 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D3-A5GR    TCGA-D3-A5GS    TCGA-D3-A5GU    TCGA-D9-A148    TCGA-D9-A149 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-D9-A1JW    TCGA-D9-A3Z1    TCGA-D9-A3Z3    TCGA-D9-A6E9    TCGA-D9-A6EA 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-D9-A6EC    TCGA-D9-A6EG    TCGA-DA-A1HV    TCGA-DA-A1HW    TCGA-DA-A1HY 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-DA-A1I0    TCGA-DA-A1I1    TCGA-DA-A1I2    TCGA-DA-A1I4    TCGA-DA-A1I5 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A1I7    TCGA-DA-A1I8    TCGA-DA-A1IA    TCGA-DA-A1IB    TCGA-DA-A1IC 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-DA-A3F2    TCGA-DA-A3F3    TCGA-DA-A3F5    TCGA-DA-A3F8    TCGA-EB-A44Q 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EB-A44R    TCGA-EB-A5KH    TCGA-EB-A5UL    TCGA-EB-A5VV    TCGA-EB-A6L9 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A17X    TCGA-EE-A17Y    TCGA-EE-A17Z    TCGA-EE-A181    TCGA-EE-A182 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A183    TCGA-EE-A185    TCGA-EE-A20B    TCGA-EE-A20C    TCGA-EE-A20F 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A20I    TCGA-EE-A29A    TCGA-EE-A29B    TCGA-EE-A29C    TCGA-EE-A29D 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29E    TCGA-EE-A29G    TCGA-EE-A29H    TCGA-EE-A29M    TCGA-EE-A29N 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29P    TCGA-EE-A29Q    TCGA-EE-A29R    TCGA-EE-A29S    TCGA-EE-A29V 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A29W    TCGA-EE-A29X    TCGA-EE-A2A0    TCGA-EE-A2A1    TCGA-EE-A2A2 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2A5    TCGA-EE-A2A6    TCGA-EE-A2GB    TCGA-EE-A2GC    TCGA-EE-A2GE 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GH    TCGA-EE-A2GI    TCGA-EE-A2GJ    TCGA-EE-A2GK    TCGA-EE-A2GL 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2GM    TCGA-EE-A2GN    TCGA-EE-A2GP    TCGA-EE-A2GR    TCGA-EE-A2GS 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A2GT    TCGA-EE-A2GU    TCGA-EE-A2M5    TCGA-EE-A2M6    TCGA-EE-A2M7 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-EE-A2M8    TCGA-EE-A2MC    TCGA-EE-A2MD    TCGA-EE-A2ME    TCGA-EE-A2MF 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MG    TCGA-EE-A2MH    TCGA-EE-A2MI    TCGA-EE-A2MJ    TCGA-EE-A2MK 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2ML    TCGA-EE-A2MM    TCGA-EE-A2MN    TCGA-EE-A2MP    TCGA-EE-A2MQ 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A2MS    TCGA-EE-A2MT    TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3AC    TCGA-EE-A3AD    TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3AH    TCGA-EE-A3J3    TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3J8    TCGA-EE-A3JA    TCGA-EE-A3JB    TCGA-EE-A3JE    TCGA-EE-A3JH 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-EE-A3JI    TCGA-ER-A195    TCGA-ER-A197    TCGA-ER-A199    TCGA-ER-A19A 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-ER-A19B    TCGA-ER-A19D    TCGA-ER-A19E    TCGA-ER-A19F    TCGA-ER-A19G 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A19H    TCGA-ER-A19J    TCGA-ER-A19M    TCGA-ER-A19O    TCGA-ER-A19P 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A19Q    TCGA-ER-A19T    TCGA-ER-A1A1    TCGA-ER-A2NC    TCGA-ER-A2ND 
 "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A2NE    TCGA-ER-A2NF    TCGA-ER-A2NG    TCGA-ER-A2NH    TCGA-ER-A3ET 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-ER-A3EV    TCGA-ER-A3PL    TCGA-ER-A42K    TCGA-ER-A42L    TCGA-FR-A3YN 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FR-A44A    TCGA-FR-A69P    TCGA-FS-A1YW    TCGA-FS-A1YX    TCGA-FS-A1YY 
"FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1Z0    TCGA-FS-A1Z3    TCGA-FS-A1Z4    TCGA-FS-A1Z7    TCGA-FS-A1ZA 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZB    TCGA-FS-A1ZC    TCGA-FS-A1ZD    TCGA-FS-A1ZE    TCGA-FS-A1ZG 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1ZH    TCGA-FS-A1ZJ    TCGA-FS-A1ZK    TCGA-FS-A1ZM    TCGA-FS-A1ZP 
 "FC.NO.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A1ZQ    TCGA-FS-A1ZR    TCGA-FS-A1ZS    TCGA-FS-A1ZT    TCGA-FS-A1ZU 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH"  "FC.NO.ENRICH" 
   TCGA-FS-A1ZW    TCGA-FS-A1ZY    TCGA-FS-A1ZZ    TCGA-FS-A4F0    TCGA-FS-A4F5 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FS-A4F8    TCGA-FS-A4F9    TCGA-FS-A4FB    TCGA-FS-A4FC    TCGA-FS-A4FD 
"FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-FW-A3I3    TCGA-FW-A3TV    TCGA-FW-A5DY    TCGA-GF-A3OT    TCGA-GF-A4EO 
 "FC.NO.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A267    TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3 
"FC.LOW.ENRICH" "FC.LOW.ENRICH" "FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
   TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS 
"FC.LOW.ENRICH"  "FC.NO.ENRICH" "FC.LOW.ENRICH" 
    clus
vv   FC.LOW.ENRICH FC.NO.ENRICH
  N0           101           40
  N1            39           14
  N2            23           11
  N3            20           15
[1] 4 2
[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   2   0
  FC.LOW.ENRICH  181  11
  FC.NO.ENRICH    73   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    2    0
  FC.LOW.ENRICH   181   11
  FC.NO.ENRICH     73    6
   clus
vv  FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  0              2           181           73
  1              0            11            6
[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  1  2
  FC.LOW.ENRICH  83 43
  FC.NO.ENRICH   23 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    1    2
  FC.LOW.ENRICH    83   43
  FC.NO.ENRICH     23   28
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO               1            83           23
  YES              2            43           28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   0   3
  FC.LOW.ENRICH   28 173
  FC.NO.ENRICH     9  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    0    3
  FC.LOW.ENRICH    28  173
  FC.NO.ENRICH      9   77
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO               0            28            9
  YES              3           173           77
[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"
D2V10, continuous
D2V11, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   1   2
  FC.LOW.ENRICH   68 133
  FC.NO.ENRICH    40  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    1    2
  FC.LOW.ENRICH    68  133
  FC.NO.ENRICH     40   46
        clus
vv       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  FEMALE              1            68           40
  MALE                2           133           46
[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"
D2V12, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   3   0
  FC.LOW.ENRICH  176  25
  FC.NO.ENRICH    75  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    3    0
  FC.LOW.ENRICH   176   25
  FC.NO.ENRICH     75   10
     clus
vv    FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  NO               3           176           75
  YES              0            25           10
[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             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.ENRICH     0                         0     3
  FC.LOW.ENRICH      1                         0   200
  FC.NO.ENRICH       4                         1    81
D2V13, multiclass
                           clus
vv                          FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  ASIAN                                  0             1            4
  BLACK OR AFRICAN AMERICAN              0             0            1
  WHITE                                  3           200           81
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   0   2
  FC.LOW.ENRICH    1 197
  FC.NO.ENRICH     2  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    0    2
  FC.LOW.ENRICH     1  197
  FC.NO.ENRICH      2   84
                        clus
vv                       FC.HIGH.ENRICH FC.LOW.ENRICH FC.NO.ENRICH
  HISPANIC OR LATINO                  0             1            2
  NOT HISPANIC OR LATINO              2           197           84
[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"
