[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/19775519/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/SKCM-TM/20278290/APOBEC_clinical_corr_input_20359542/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   73  131 
   0 HIGH  LOW 
  86   73  131 
[1] "APOBEC_ENRICH"
[1] 3
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            3            82           205 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            3            82           205 
[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=156,	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=162,	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 58 58 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53    62    58    58 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
23 30 62 58 58 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53    62    58    58 
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 34
  HIGH 25 22
  LOW  49 45
   0 HIGH  LOW 
  55   47   94 
   0 HIGH  LOW 
  34   22   45 
$`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        16.96         9.34 
TCGA-D3-A51E TCGA-D3-A51K TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A3F2 
      173.85        31.76        22.29        22.85       138.67        30.44 
TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A29P 
        3.91        50.07        52.41        18.21        67.50        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         1.58         7.82        53.29       151.46        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        47.97         4.70        16.87 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZG 
      173.29        68.52       171.78        49.74        27.62         7.82 
TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-GN-A265 
       36.33        78.61        35.28         4.47         5.29        96.92 
TCGA-RP-A690 
        0.20 

$HIGH
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A3C7 TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A51R 
       49.35        62.86        46.98        13.87        90.21        62.70 
TCGA-D3-A51T TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X 
       11.34        69.21        76.34        58.85        14.96        13.15 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       20.38         0.00        75.55        75.22        12.99         0.26 
TCGA-EE-A29M TCGA-EE-A2A2 TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR 
       47.74        30.02        68.65        18.35       118.32         0.20 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      209.79       171.85        63.25        25.08       143.93        23.51 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J7 TCGA-EE-A3JB 
       53.26       124.31        64.04        54.51        45.90       201.80 
TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A1ZQ TCGA-FS-A1ZW 
      152.81        14.56        74.47         8.35       130.95        23.21 
TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3TU TCGA-GN-A4U4 TCGA-QB-A6FS 
        3.06        80.68        55.59        34.49         7.23 

$LOW
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2JA 
       31.89        19.04        76.41        62.60        45.99        15.75 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3CB 
       36.30       171.58        64.83        66.08        43.53       140.98 
TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GR 
       40.01        23.67       144.46        42.05        45.70       177.86 
TCGA-D9-A3Z1 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA 
       15.02        53.65       150.61        95.51        45.07        64.83 
TCGA-DA-A3F5 TCGA-EB-A5SG TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A20H TCGA-EE-A29C 
      225.11        33.24        24.89        62.37       155.90        76.14 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 
       44.28        63.12        61.12       346.49       115.43        77.98 
TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GN 
       26.14       239.11        12.95       201.60        32.48        31.00 
TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MK 
        0.76        81.99       103.13         5.75        23.77        89.26 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
      104.78       145.45       122.73         4.41         6.28       111.85 
TCGA-EE-A3J8 TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C 
        3.35        19.86        34.45        47.31         4.54        39.81 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC 
       11.47       150.12        59.84        42.48       146.63        22.36 
TCGA-ER-A2NG TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1ZC 
       10.95        15.48        32.05       174.21       195.98       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F4 
       32.78        42.08        12.92       136.27        18.51        66.67 
TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
      173.19        13.28        11.54        19.30         9.90         6.05 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        1.91        53.29       117.93        17.06        42.48         7.59 
TCGA-GN-A4U3 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A693 
      120.53        46.92       297.01         0.33 

   0 HIGH  LOW 
0.20 0.00 0.33 
     0   HIGH    LOW 
227.01 209.79 346.49 
     0   HIGH    LOW 
49.710 53.260 45.385 
[1] "0.2 - 227.0 (49.7)" "0.0 - 209.8 (53.3)" "0.3 - 346.5 (45.4)"
D1V2, survival
      sevent
clus2   0  1
  0    33 51
  HIGH 36 34
  LOW  60 70
   0 HIGH  LOW 
  84   70  130 
   0 HIGH  LOW 
  51   34   70 
$`0`
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.57        16.67       112.57       133.25        31.59        43.43 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3BZ TCGA-D3-A3C6 
       23.77       168.00        86.76       113.52       130.72        58.06 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H 
       60.23        24.53         9.34       174.84        55.73        56.35 
TCGA-D3-A51K TCGA-D3-A51N TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY 
       32.94        22.62        54.67        22.29        22.95       144.89 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R 
       20.38        35.93        40.60        33.93        13.87        10.36 
TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z 
       20.35        54.02        58.92         7.04        36.46         8.65 
TCGA-EE-A184 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GK 
       68.15       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       268.93 
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        79.99 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FR-A69P 
       23.34        20.15        16.37       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         0.20        96.92        48.00        22.13         0.20 

$HIGH
TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-D3-A2JF TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3ML 
       71.80        65.49        62.07        46.98        46.32        13.87 
TCGA-D3-A3MR TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GU 
      103.59        45.30        63.81        26.89       137.92       125.19 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A17X 
       25.18        77.56        76.57        68.09        15.68        29.82 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
       33.73        14.70       151.27        85.08        13.97        63.78 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GI 
        2.60        56.84        61.28        59.64        67.43        48.72 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2M5 TCGA-EE-A2MD 
      107.38        75.48       126.81        42.77        21.67        47.28 
TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
      268.73       204.66        96.23       134.40       162.48        71.21 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3J5 
       53.26       124.31        64.04        54.51        41.59        36.95 
TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A193 
       64.08        53.19       201.80        27.35       152.81        31.40 
TCGA-ER-A19F TCGA-ER-A42L TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       26.37       149.03        20.91        27.72        23.93       133.55 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GF-A6C9 
       49.48        27.02        80.68        22.92        55.59        15.78 
TCGA-GN-A266 TCGA-GN-A4U4 TCGA-QB-A6FS TCGA-RP-A694 
       10.13        39.35         7.23         0.69 

$LOW
TCGA-D3-A1Q4 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2JA 
      112.04        28.08        90.90        95.74       103.10       115.53 
TCGA-D3-A2JD TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       11.87        42.08        12.10       171.58        66.48        66.08 
TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A5GL 
       59.57       166.52        86.93        39.75       145.12       125.79 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX 
      135.75       178.32        18.18       151.53         3.65         7.10 
TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 
       15.39         9.90        36.03       207.48       176.55       120.00 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A5SG 
       73.84        53.92        65.92        10.49       225.96        68.25 
TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       29.29        27.22        94.98        26.89         4.96        91.56 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29N 
      168.26        63.35        78.97        72.07        64.64        18.61 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       66.74        14.47       369.93        25.87        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.96        39.29        86.14        59.28       340.14       173.79 
TCGA-EE-A2GH TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GU TCGA-EE-A2M6 
      220.24        79.66       102.12        13.91        94.82       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-A3AF TCGA-EE-A3AH TCGA-EE-A3J4 
       43.23       122.73        28.77        13.81       138.81       127.20 
TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A 
       34.32        51.35       134.33        35.44        50.76        77.75 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M 
       48.89        12.59        13.02       152.35         6.44        61.05 
TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV 
       44.05       148.18        43.82        31.27        32.05        46.98 
TCGA-ER-A3PL TCGA-ER-A42K TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z7 
       33.21        12.95        92.98       174.21       202.65         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZP 
       48.85       357.37        53.52        46.45        15.45        74.73 
TCGA-FS-A1ZS TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
      148.80        77.82        66.67        28.73       174.84        34.03 
TCGA-FS-A4FC TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 
       54.41        13.51        19.30         9.90         7.23         2.04 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A4U3 
      139.89       117.93        64.44        62.79        32.48       121.91 
TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-OD-A75X TCGA-RP-A693 
       10.42        48.89       297.90         0.33 

   0 HIGH  LOW 
0.20 0.69 0.33 
     0   HIGH    LOW 
268.93 268.73 369.93 
    0  HIGH   LOW 
46.13 55.05 62.15 
[1] "0.2 - 268.9 (46.1)" "0.7 - 268.7 (55.0)" "0.3 - 369.9 (62.1)"
D1V3, continuous
      vv
clus   I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  0              3       3       7        0        6        3         2
  HIGH           2       2       5        6        5        8         3
  LOW            5       1      13        4       14        7         5
      vv
clus   STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  0            4         5        10          3          8         16        6
  HIGH         5         1        11          2          8          9        3
  LOW          5         4        16          9          8         19        7
D1V4, multiclass
             clus
vv             0 HIGH LOW
  I OR II NOS  3    2   5
  STAGE 0      3    2   1
  STAGE I      7    5  13
  STAGE IA     0    6   4
  STAGE IB     6    5  14
  STAGE II     3    8   7
  STAGE IIA    2    3   5
  STAGE IIB    4    5   5
  STAGE IIC    5    1   4
  STAGE III   10   11  16
  STAGE IIIA   3    2   9
  STAGE IIIB   8    8   8
  STAGE IIIC  16    9  19
  STAGE IV     6    3   7
[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 13 22
  HIGH    14 15 17 14
  LOW     28 30 28 22
D1V5, multiclass
       clus
vv       0 HIGH LOW
  T0+T1 11   14  28
  T2    17   15  30
  T3    13   17  28
  T4    22   14  22
[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 39 12 11  5
  LOW  64 27 12 15
D1V6, multiclass
    clus
vv    0 HIGH LOW
  N0 40   39  64
  N1 14   12  27
  N2 11   11  12
  N3 15    5  15
[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  67   3
  LOW  116   8
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      73    6
  HIGH   67    3
  LOW   116    8
   clus
vv    0 HIGH LOW
  0  73   67 116
  1   6    3   8
[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 28 15
  LOW  56 30
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      23   28
  HIGH   28   15
  LOW    56   30
     clus
vv     0 HIGH LOW
  NO  23   28  56
  YES 28   15  30
[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  12  61
  LOW   16 115
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       9   77
  HIGH   12   61
  LOW    16  115
     clus
vv      0 HIGH LOW
  NO    9   12  16
  YES  77   61 115
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, binary
      cls
clus    0  1
  0    40 46
  HIGH 18 55
  LOW  51 80
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      40   46
  HIGH   18   55
  LOW    51   80
        clus
vv        0 HIGH LOW
  FEMALE 40   18  51
  MALE   46   55  80
[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     74  10
  HIGH  64   9
  LOW  115  16
[1] "tbl2"
      cls
clus   [,1] [,2]
  0      74   10
  HIGH   64    9
  LOW   115   16
     clus
vv      0 HIGH LOW
  NO   74   64 115
  YES  10    9  16
[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    73
  LOW      1                         0   130
D1V13, multiclass
                           clus
vv                            0 HIGH LOW
  ASIAN                       4    0   1
  BLACK OR AFRICAN AMERICAN   1    0   0
  WHITE                      81   73 130
[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  71
  LOW    0 128
[1] "tbl2"
      cls
clus   [,1] [,2]
  0       2   84
  HIGH    1   71
  LOW     0  128
                        clus
vv                         0 HIGH LOW
  HISPANIC OR LATINO       2    1   0
  NOT HISPANIC OR LATINO  84   71 128
[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    1  2
  FC.LOW.NONSIG 19 33
  FC.NEUTRAL    75 66
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            3            52           141 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            2            33            66 
$FC.HIGH.SIG
TCGA-D3-A3CC TCGA-FS-A4F4 TCGA-GN-A264 
       40.01        66.67       117.93 

$FC.LOW.NONSIG
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-A3MO TCGA-D3-A51E 
       86.30       107.61        58.06        59.70         9.34       173.85 
TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A5SH 
       22.29        22.85       138.67        30.44         3.91        50.07 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A184 TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GS 
       52.41        18.21        67.50        27.16       185.19        71.31 
TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 
       15.25        94.19       227.01        67.89         1.58         7.82 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       53.29       151.46        99.06       120.76        49.71        47.18 
TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3ET TCGA-FS-A1YW 
       47.97         4.70        16.87       173.29        68.52       171.78 
TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZT 
       49.74        27.62         7.82        36.33        78.61        35.28 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-GN-A265 TCGA-RP-A690 
        4.47         5.29        96.92         0.20 

$FC.NEUTRAL
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       31.89        49.35        19.04        76.41        62.60        45.99 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO 
       62.86        15.75        36.30       171.58        64.83        66.08 
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR 
       43.53        46.98       140.98        16.96        13.87        90.21 
TCGA-D3-A3MU TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL 
       23.67       144.46        31.76        62.70        11.34        42.05 
TCGA-D3-A5GN TCGA-D3-A5GR TCGA-D9-A3Z1 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1I1 
       45.70       177.86        15.02        69.21        76.34        53.65 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F5 
      150.61        95.51        45.07        64.83        58.85       225.11 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 
       14.96        33.24        13.15        24.89        62.37        20.38 
TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D 
        0.00        75.55       155.90        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        63.12        47.74        61.12       346.49 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GD TCGA-EE-A2GE 
      115.43        30.02        77.98        26.14       239.11        12.95 
TCGA-EE-A2GH TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
      201.60        68.65        10.62        32.48        18.35        31.00 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M8 
      118.32         0.76         0.20        81.99       103.13         5.75 
TCGA-EE-A2MC TCGA-EE-A2MF TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
       23.77       209.79       171.85        63.25        89.26       104.78 
TCGA-EE-A2MM TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
      145.45        25.08       143.93        23.51        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3J4 
      122.73        64.04         4.41        54.51         6.28       111.85 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JB TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
       45.90         3.35       201.80        19.86       152.81        14.56 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19H 
       34.45        47.31         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        42.48       146.63        22.36        10.95        15.48 
TCGA-ER-A3PL TCGA-ER-A42L TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1ZC 
       32.05        74.47       174.21       195.98         8.35       312.07 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW 
       32.78        42.08        12.92       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         6.05         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.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        40.01          0.20          0.00 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       117.93        227.01        346.49 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       66.670        49.905        45.990 
[1] "40.0 - 117.9 (66.7)" "0.2 - 227.0 (49.9)"  "0.0 - 346.5 (46.0)" 
D2V2, survival
               sevent
clus2             0   1
  FC.HIGH.SIG     1   2
  FC.LOW.NONSIG  31  49
  FC.NEUTRAL     97 104
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            3            80           201 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            2            49           104 
$FC.HIGH.SIG
TCGA-D3-A3CC TCGA-FS-A4F4 TCGA-GN-A264 
       86.93        66.67       117.93 

$FC.LOW.NONSIG
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.57        16.67       112.57       133.25        31.59        43.43 
TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JG TCGA-D3-A3BZ TCGA-D3-A3C6 
       23.77       168.00        86.76       113.52       130.72        58.06 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N 
       60.23         9.34       174.84        55.73        56.35        22.62 
TCGA-D9-A149 TCGA-D9-A3Z3 TCGA-D9-A6EG TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 
       54.67        22.29        22.95       144.89        20.38        35.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       40.60        33.93        13.87        10.36        20.35        54.02 
TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17Z TCGA-EE-A184 TCGA-EE-A20B 
       58.92         7.04        36.46         8.65        68.15       133.81 
TCGA-EE-A29P TCGA-EE-A29W TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2ME 
       56.42       195.02        81.21        44.88        28.83       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3J3 TCGA-ER-A197 TCGA-ER-A199 
      103.20        16.96       248.65       172.18        13.94         9.17 
TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       98.40       268.93       131.51       162.08        50.89        49.48 
TCGA-ER-A19T TCGA-ER-A1A1 TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
        8.88        79.99        23.34        20.15        16.37       247.04 
TCGA-ER-A3ET TCGA-FR-A69P TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z4 
       93.01        15.72       216.92        48.59       228.59        28.08 
TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZT 
        9.70        32.75        47.38       101.26        11.41        53.16 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D 
       26.56        27.09        26.73         0.20        96.92        48.00 
TCGA-GN-A4U9 TCGA-RP-A690 
       22.13         0.20 

$FC.NEUTRAL
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
      112.04        71.80        28.08        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2JA TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JK 
       65.49       115.53        11.87        62.07        42.08        12.10 
TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A3C8 
      171.58        66.48        66.08        59.57        46.98        46.32 
TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
      166.52        24.53        13.87       103.59        39.75        45.30 
TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN 
      145.12        32.94        63.81        26.89       125.79       135.75 
TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW 
      137.92       178.32        18.18       125.19       151.53         3.65 
TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV 
        7.10        15.39         9.90        25.18        77.56        76.57 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03       207.48       176.55       120.00        73.84        53.92 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       65.92        68.09        10.49       225.96        15.68        68.25 
TCGA-EB-A5UL TCGA-EE-A17X TCGA-EE-A17Y TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 
       29.29        29.82        27.22        94.98        33.73        14.70 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A20I 
       26.89         4.96       151.27        91.56       168.26        13.55 
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-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       64.64         2.60        56.84        18.61        66.74        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       61.28       369.93        25.87        17.92        46.82       115.96 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       59.64        39.29        86.14        59.28        67.43       340.14 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      173.79       220.24        48.72       107.38        54.74        79.66 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GU 
       75.48       102.12       126.81        13.91        42.77        94.82 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2MF 
       21.67       129.27        19.76        61.51        47.28       268.73 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      204.66        96.23       180.39       216.66       167.90        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
       43.23       134.40       162.48        71.21        53.26       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
      122.73        64.04        28.77        54.51        13.81        41.59 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA 
      138.81       127.20        36.95        64.08        34.32        53.19 
TCGA-EE-A3JB TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 
      201.80        27.35        51.35       134.33       152.81        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A19A TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
       35.44        50.76        77.75        48.89        12.59        13.02 
TCGA-ER-A19F TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19W 
       26.37       152.35         6.44        61.05        44.05       148.18 
TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3EV TCGA-ER-A3PL TCGA-ER-A42K 
       43.82        31.27        32.05        46.98        33.21        12.95 
TCGA-ER-A42L TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
      149.03        92.98       174.21       202.65        20.91         7.79 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF 
       27.72        48.85       357.37        53.52        46.45        15.45 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       23.93        74.73       133.55       148.80        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FS-A4FD 
       77.82        28.73       174.84        34.03        54.41        80.68 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       22.92        55.59        13.51        19.30         9.90         7.23 
TCGA-GF-A6C8 TCGA-GF-A6C9 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        2.04        15.78       139.89        10.13        64.44        62.79 
TCGA-GN-A26A TCGA-GN-A4U3 TCGA-GN-A4U4 TCGA-GN-A4U7 TCGA-GN-A4U8 TCGA-OD-A75X 
       32.48       121.91        39.35        10.42        48.89       297.90 
TCGA-QB-A6FS TCGA-RP-A693 TCGA-RP-A694 
        7.23         0.33         0.69 

  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        66.67          0.20          0.33 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
       117.93        268.93        369.93 
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
        86.93         47.69         55.59 
[1] "66.7 - 117.9 (86.9)" "0.2 - 268.9 (47.7)"  "0.3 - 369.9 (55.6)" 
D2V3, continuous
               vv
clus            I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II
  FC.HIGH.SIG             0       0       0        0        0        1
  FC.LOW.NONSIG           3       3       6        0        6        3
  FC.NEUTRAL              7       3      19       10       19       14
               vv
clus            STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  FC.HIGH.SIG           0         0         1         0          0          0
  FC.LOW.NONSIG         2         4         5        10          3          7
  FC.NEUTRAL            8        10         4        27         11         17
               vv
clus            STAGE IIIC STAGE IV
  FC.HIGH.SIG            0        0
  FC.LOW.NONSIG         15        5
  FC.NEUTRAL            29       11
D2V4, multiclass
[1] "Remove cluster labels:" "FC.HIGH.SIG"           
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            2            72           189 
   TCGA-D3-A1Q1    TCGA-D3-A1Q3    TCGA-D3-A1Q4    TCGA-D3-A1Q5    TCGA-D3-A1Q6 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A1Q7    TCGA-D3-A1Q8    TCGA-D3-A1Q9    TCGA-D3-A1QA    TCGA-D3-A1QB 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A2J6    TCGA-D3-A2J7    TCGA-D3-A2J8    TCGA-D3-A2J9    TCGA-D3-A2JA 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A2JB    TCGA-D3-A2JC    TCGA-D3-A2JD    TCGA-D3-A2JF    TCGA-D3-A2JG 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A2JH    TCGA-D3-A2JK    TCGA-D3-A2JL    TCGA-D3-A2JN    TCGA-D3-A2JO 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A2JP    TCGA-D3-A3BZ    TCGA-D3-A3C1    TCGA-D3-A3C3    TCGA-D3-A3C6 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A3C7    TCGA-D3-A3C8    TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A3ML    TCGA-D3-A3MO    TCGA-D3-A3MR    TCGA-D3-A3MU    TCGA-D3-A3MV 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A51E    TCGA-D3-A51F    TCGA-D3-A51G    TCGA-D3-A51H    TCGA-D3-A51J 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A51K    TCGA-D3-A51N    TCGA-D3-A51R    TCGA-D3-A51T    TCGA-D3-A5GL 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A5GN    TCGA-D3-A5GO    TCGA-D3-A5GR    TCGA-D3-A5GS    TCGA-D3-A5GU 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D9-A3Z1    TCGA-D9-A3Z3    TCGA-D9-A6E9    TCGA-D9-A6EA    TCGA-D9-A6EC 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D9-A6EG    TCGA-DA-A1HV    TCGA-DA-A1HW    TCGA-DA-A1HY    TCGA-DA-A1I0 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-DA-A1I1    TCGA-DA-A1I2    TCGA-DA-A1I4    TCGA-DA-A1I5    TCGA-DA-A1I7 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-DA-A1I8    TCGA-DA-A1IA    TCGA-DA-A1IB    TCGA-DA-A1IC    TCGA-DA-A3F2 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-DA-A3F3    TCGA-DA-A3F5    TCGA-DA-A3F8    TCGA-EB-A44Q    TCGA-EB-A44R 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EB-A5KH    TCGA-EB-A5SH    TCGA-EB-A5UL    TCGA-EB-A5UN    TCGA-EB-A5VV 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EB-A6L9    TCGA-EE-A17X    TCGA-EE-A17Y    TCGA-EE-A17Z    TCGA-EE-A180 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A183    TCGA-EE-A184    TCGA-EE-A185 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A20B    TCGA-EE-A20C    TCGA-EE-A20F    TCGA-EE-A20H    TCGA-EE-A20I 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29A    TCGA-EE-A29B    TCGA-EE-A29C    TCGA-EE-A29D    TCGA-EE-A29E 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29G    TCGA-EE-A29H    TCGA-EE-A29L    TCGA-EE-A29M    TCGA-EE-A29N 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29P    TCGA-EE-A29Q    TCGA-EE-A29R    TCGA-EE-A29S    TCGA-EE-A29V 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29W    TCGA-EE-A29X    TCGA-EE-A2A0    TCGA-EE-A2A1    TCGA-EE-A2A2 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2A5    TCGA-EE-A2A6    TCGA-EE-A2GB    TCGA-EE-A2GC    TCGA-EE-A2GD 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GE    TCGA-EE-A2GH    TCGA-EE-A2GI    TCGA-EE-A2GJ    TCGA-EE-A2GK 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GL    TCGA-EE-A2GM    TCGA-EE-A2GN    TCGA-EE-A2GO    TCGA-EE-A2GP 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GR    TCGA-EE-A2GS    TCGA-EE-A2GT    TCGA-EE-A2GU    TCGA-EE-A2M5 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2M6    TCGA-EE-A2M7    TCGA-EE-A2M8    TCGA-EE-A2MC    TCGA-EE-A2MD 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2ME    TCGA-EE-A2MF    TCGA-EE-A2MG    TCGA-EE-A2MH    TCGA-EE-A2MI 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A2MJ    TCGA-EE-A2MK    TCGA-EE-A2ML    TCGA-EE-A2MM    TCGA-EE-A2MN 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MP    TCGA-EE-A2MQ    TCGA-EE-A2MR    TCGA-EE-A2MS    TCGA-EE-A2MT 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB    TCGA-EE-A3AC    TCGA-EE-A3AD 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG    TCGA-EE-A3AH    TCGA-EE-A3J3 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7    TCGA-EE-A3J8    TCGA-EE-A3JA 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3JB    TCGA-EE-A3JD    TCGA-EE-A3JE    TCGA-EE-A3JH    TCGA-EE-A3JI 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A193    TCGA-ER-A197    TCGA-ER-A199    TCGA-ER-A19A    TCGA-ER-A19C 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A19D    TCGA-ER-A19E    TCGA-ER-A19J    TCGA-ER-A19M    TCGA-ER-A19O 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-ER-A19T    TCGA-ER-A1A1    TCGA-ER-A2NC    TCGA-ER-A2ND    TCGA-ER-A2NE 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-ER-A2NF    TCGA-ER-A2NG    TCGA-ER-A2NH    TCGA-ER-A3ET    TCGA-ER-A3EV 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-ER-A3PL    TCGA-ER-A42K    TCGA-ER-A42L    TCGA-FR-A3YN    TCGA-FR-A3YO 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FR-A44A    TCGA-FR-A69P    TCGA-FS-A1YW    TCGA-FS-A1YX    TCGA-FS-A1YY 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-FS-A1Z0    TCGA-FS-A1Z3    TCGA-FS-A1Z4    TCGA-FS-A1Z7    TCGA-FS-A1ZA 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1ZB    TCGA-FS-A1ZC    TCGA-FS-A1ZD    TCGA-FS-A1ZE    TCGA-FS-A1ZF 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1ZG    TCGA-FS-A1ZH    TCGA-FS-A1ZJ    TCGA-FS-A1ZK    TCGA-FS-A1ZM 
"FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FS-A1ZP    TCGA-FS-A1ZQ    TCGA-FS-A1ZR    TCGA-FS-A1ZS    TCGA-FS-A1ZT 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FS-A1ZU    TCGA-FS-A1ZW    TCGA-FS-A1ZY    TCGA-FS-A1ZZ    TCGA-FS-A4F0 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A4F5    TCGA-FS-A4F8    TCGA-FS-A4F9    TCGA-FS-A4FB    TCGA-FS-A4FC 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-FS-A4FD    TCGA-FW-A3I3    TCGA-FW-A3R5    TCGA-FW-A3TV    TCGA-FW-A5DY 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-GF-A3OT    TCGA-GF-A4EO    TCGA-GF-A6C8    TCGA-GF-A6C9    TCGA-GN-A267 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3    TCGA-GN-A4U4 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS    TCGA-RP-A693    TCGA-RP-A694 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-RP-A695 
   "FC.NEUTRAL" 
             clus
vv            FC.LOW.NONSIG FC.NEUTRAL
  I OR II NOS             3          7
  STAGE 0                 3          3
  STAGE I                 6         19
  STAGE IA                0         10
  STAGE IB                6         19
  STAGE II                3         14
  STAGE IIA               2          8
  STAGE IIB               4         10
  STAGE IIC               5          4
  STAGE III              10         27
  STAGE IIIA              3         11
  STAGE IIIB              7         17
  STAGE IIIC             15         29
  STAGE IV                5         11
[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.SIG       0  0  1  1
  FC.LOW.NONSIG    10 17 13 21
  FC.NEUTRAL       43 45 44 36
D2V5, multiclass
[1] "Remove cluster labels:" "FC.HIGH.SIG"           
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            2            61           168 
   TCGA-D3-A1Q1    TCGA-D3-A1Q3    TCGA-D3-A1Q4    TCGA-D3-A1Q6    TCGA-D3-A1Q7 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A1Q8    TCGA-D3-A1Q9    TCGA-D3-A1QA    TCGA-D3-A1QB    TCGA-D3-A2J6 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A2J7    TCGA-D3-A2J8    TCGA-D3-A2J9    TCGA-D3-A2JA    TCGA-D3-A2JC 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A2JD    TCGA-D3-A2JF    TCGA-D3-A2JG    TCGA-D3-A2JH    TCGA-D3-A2JK 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A2JN    TCGA-D3-A2JP    TCGA-D3-A3BZ    TCGA-D3-A3C6    TCGA-D3-A3C7 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF    TCGA-D3-A3ML    TCGA-D3-A3MR 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A3MU    TCGA-D3-A3MV    TCGA-D3-A51E    TCGA-D3-A51F    TCGA-D3-A51H 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-D3-A51J    TCGA-D3-A51N    TCGA-D3-A51R    TCGA-D3-A51T    TCGA-D3-A5GL 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A5GN    TCGA-D3-A5GO    TCGA-D3-A5GR    TCGA-D3-A5GS    TCGA-D3-A5GU 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D9-A1JW    TCGA-D9-A3Z1    TCGA-D9-A3Z3    TCGA-D9-A6E9    TCGA-D9-A6EA 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D9-A6EC    TCGA-D9-A6EG    TCGA-DA-A1HV    TCGA-DA-A1HW    TCGA-DA-A1HY 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-DA-A1I0    TCGA-DA-A1I1    TCGA-DA-A1I2    TCGA-DA-A1I4    TCGA-DA-A1I5 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-DA-A1I7    TCGA-DA-A1I8    TCGA-DA-A1IA    TCGA-DA-A1IB    TCGA-DA-A1IC 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-DA-A3F2    TCGA-DA-A3F3    TCGA-DA-A3F5    TCGA-DA-A3F8    TCGA-EB-A5KH 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-EB-A5SH    TCGA-EB-A5UN    TCGA-EB-A5VV    TCGA-EE-A17X    TCGA-EE-A17Y 
"FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A17Z    TCGA-EE-A180    TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A184 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-EE-A185    TCGA-EE-A20B    TCGA-EE-A20F    TCGA-EE-A20H    TCGA-EE-A29A 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29B    TCGA-EE-A29C    TCGA-EE-A29D    TCGA-EE-A29E    TCGA-EE-A29G 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29H    TCGA-EE-A29L    TCGA-EE-A29M    TCGA-EE-A29P    TCGA-EE-A29Q 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A29R    TCGA-EE-A29S    TCGA-EE-A29V    TCGA-EE-A29X    TCGA-EE-A2A0 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2A1    TCGA-EE-A2A2    TCGA-EE-A2A5    TCGA-EE-A2A6    TCGA-EE-A2GB 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GC    TCGA-EE-A2GD    TCGA-EE-A2GE    TCGA-EE-A2GH    TCGA-EE-A2GI 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GJ    TCGA-EE-A2GK    TCGA-EE-A2GL    TCGA-EE-A2GM    TCGA-EE-A2GN 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GO    TCGA-EE-A2GP    TCGA-EE-A2GR    TCGA-EE-A2GS    TCGA-EE-A2GT 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EE-A2GU    TCGA-EE-A2M5    TCGA-EE-A2M6    TCGA-EE-A2M7    TCGA-EE-A2M8 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A2MC    TCGA-EE-A2MD    TCGA-EE-A2ME    TCGA-EE-A2MF    TCGA-EE-A2MG 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-EE-A2MH    TCGA-EE-A2MI    TCGA-EE-A2MJ    TCGA-EE-A2MK    TCGA-EE-A2ML 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MM    TCGA-EE-A2MN    TCGA-EE-A2MP    TCGA-EE-A2MQ    TCGA-EE-A2MR 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MS    TCGA-EE-A2MT    TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3AC    TCGA-EE-A3AD    TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3AH    TCGA-EE-A3J3    TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3J8    TCGA-EE-A3JA    TCGA-EE-A3JB    TCGA-EE-A3JE    TCGA-EE-A3JH 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3JI    TCGA-ER-A193    TCGA-ER-A197    TCGA-ER-A199    TCGA-ER-A19C 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-ER-A19D    TCGA-ER-A19E    TCGA-ER-A19M    TCGA-ER-A19O    TCGA-ER-A19T 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-ER-A2NC    TCGA-ER-A2ND    TCGA-ER-A2NF    TCGA-ER-A2NG    TCGA-ER-A2NH 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A3ET    TCGA-ER-A3EV    TCGA-ER-A3PL    TCGA-ER-A42K    TCGA-ER-A42L 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FR-A3YN    TCGA-FR-A3YO    TCGA-FR-A44A    TCGA-FS-A1YW    TCGA-FS-A1YX 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-FS-A1YY    TCGA-FS-A1Z0    TCGA-FS-A1Z4    TCGA-FS-A1Z7    TCGA-FS-A1ZA 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1ZB    TCGA-FS-A1ZD    TCGA-FS-A1ZE    TCGA-FS-A1ZF    TCGA-FS-A1ZG 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FS-A1ZH    TCGA-FS-A1ZJ    TCGA-FS-A1ZK    TCGA-FS-A1ZM    TCGA-FS-A1ZP 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-FS-A1ZR    TCGA-FS-A1ZS    TCGA-FS-A1ZT    TCGA-FS-A1ZU    TCGA-FS-A1ZW 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-FS-A1ZY    TCGA-FS-A1ZZ    TCGA-FS-A4F0    TCGA-FS-A4F5    TCGA-FS-A4F8 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A4F9    TCGA-FS-A4FB    TCGA-FS-A4FC    TCGA-FS-A4FD    TCGA-FW-A3I3 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FW-A3TV    TCGA-FW-A5DY    TCGA-GF-A3OT    TCGA-GF-A4EO    TCGA-GF-A6C8 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-GN-A267    TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-GN-A4U4    TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
       clus
vv      FC.LOW.NONSIG FC.NEUTRAL
  T0+T1            10         43
  T2               17         45
  T3               13         44
  T4               21         36
[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.SIG     2   0   0   0
  FC.LOW.NONSIG  38  14  10  14
  FC.NEUTRAL    103  39  24  21
D2V6, multiclass
[1] "Remove cluster labels:" "FC.HIGH.SIG"           
clus
  FC.HIGH.SIG FC.LOW.NONSIG    FC.NEUTRAL 
            2            76           187 
   TCGA-D3-A1Q1    TCGA-D3-A1Q3    TCGA-D3-A1Q4    TCGA-D3-A1Q5    TCGA-D3-A1Q6 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A1Q7    TCGA-D3-A1Q8    TCGA-D3-A1Q9    TCGA-D3-A1QA    TCGA-D3-A1QB 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A2J6    TCGA-D3-A2J7    TCGA-D3-A2J8    TCGA-D3-A2J9    TCGA-D3-A2JA 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A2JB    TCGA-D3-A2JC    TCGA-D3-A2JD    TCGA-D3-A2JF    TCGA-D3-A2JG 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A2JH    TCGA-D3-A2JK    TCGA-D3-A2JL    TCGA-D3-A2JN    TCGA-D3-A2JO 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A2JP    TCGA-D3-A3BZ    TCGA-D3-A3C1    TCGA-D3-A3C3    TCGA-D3-A3C6 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D3-A3C7    TCGA-D3-A3C8    TCGA-D3-A3CB    TCGA-D3-A3CE    TCGA-D3-A3CF 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A3ML    TCGA-D3-A3MO    TCGA-D3-A3MR    TCGA-D3-A3MU    TCGA-D3-A3MV 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A51E    TCGA-D3-A51F    TCGA-D3-A51G    TCGA-D3-A51H    TCGA-D3-A51J 
"FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-D3-A51K    TCGA-D3-A51N    TCGA-D3-A51R    TCGA-D3-A51T    TCGA-D3-A5GL 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D3-A5GN    TCGA-D3-A5GO    TCGA-D3-A5GR    TCGA-D3-A5GS    TCGA-D3-A5GU 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-D9-A148    TCGA-D9-A149    TCGA-D9-A1JW    TCGA-D9-A3Z1    TCGA-D9-A3Z3 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-D9-A6E9    TCGA-D9-A6EA    TCGA-D9-A6EC    TCGA-D9-A6EG    TCGA-DA-A1HV 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-DA-A1HW    TCGA-DA-A1HY    TCGA-DA-A1I0    TCGA-DA-A1I1    TCGA-DA-A1I2 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-DA-A1I4    TCGA-DA-A1I5    TCGA-DA-A1I7    TCGA-DA-A1I8    TCGA-DA-A1IA 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-DA-A1IB    TCGA-DA-A1IC    TCGA-DA-A3F2    TCGA-DA-A3F3    TCGA-DA-A3F5 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-DA-A3F8    TCGA-EB-A44Q    TCGA-EB-A44R    TCGA-EB-A5KH    TCGA-EB-A5SH 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EB-A5UL    TCGA-EB-A5VV    TCGA-EB-A6L9    TCGA-EE-A17X    TCGA-EE-A17Y 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A17Z    TCGA-EE-A180    TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A183 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A184    TCGA-EE-A185    TCGA-EE-A20B    TCGA-EE-A20C    TCGA-EE-A20F 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A20H    TCGA-EE-A20I    TCGA-EE-A29A    TCGA-EE-A29B    TCGA-EE-A29C 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29D    TCGA-EE-A29E    TCGA-EE-A29G    TCGA-EE-A29H    TCGA-EE-A29L 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29M    TCGA-EE-A29N    TCGA-EE-A29P    TCGA-EE-A29Q    TCGA-EE-A29R 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A29S    TCGA-EE-A29V    TCGA-EE-A29W    TCGA-EE-A29X    TCGA-EE-A2A0 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2A1    TCGA-EE-A2A2    TCGA-EE-A2A5    TCGA-EE-A2A6    TCGA-EE-A2GB 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GC    TCGA-EE-A2GD    TCGA-EE-A2GE    TCGA-EE-A2GH    TCGA-EE-A2GI 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GJ    TCGA-EE-A2GK    TCGA-EE-A2GL    TCGA-EE-A2GM    TCGA-EE-A2GN 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2GO    TCGA-EE-A2GP    TCGA-EE-A2GR    TCGA-EE-A2GS    TCGA-EE-A2GT 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-EE-A2GU    TCGA-EE-A2M5    TCGA-EE-A2M6    TCGA-EE-A2M7    TCGA-EE-A2M8 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-EE-A2MC    TCGA-EE-A2MD    TCGA-EE-A2ME    TCGA-EE-A2MF    TCGA-EE-A2MG 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-EE-A2MH    TCGA-EE-A2MI    TCGA-EE-A2MJ    TCGA-EE-A2MK    TCGA-EE-A2ML 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MM    TCGA-EE-A2MN    TCGA-EE-A2MP    TCGA-EE-A2MQ    TCGA-EE-A2MR 
   "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A2MS    TCGA-EE-A2MT    TCGA-EE-A2MU    TCGA-EE-A3AA    TCGA-EE-A3AB 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3AC    TCGA-EE-A3AD    TCGA-EE-A3AE    TCGA-EE-A3AF    TCGA-EE-A3AG 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3AH    TCGA-EE-A3J3    TCGA-EE-A3J4    TCGA-EE-A3J5    TCGA-EE-A3J7 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3J8    TCGA-EE-A3JA    TCGA-EE-A3JB    TCGA-EE-A3JD    TCGA-EE-A3JE 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-EE-A3JH    TCGA-EE-A3JI    TCGA-ER-A193    TCGA-ER-A195    TCGA-ER-A197 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-ER-A199    TCGA-ER-A19A    TCGA-ER-A19B    TCGA-ER-A19D    TCGA-ER-A19E 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A19F    TCGA-ER-A19G    TCGA-ER-A19H    TCGA-ER-A19J    TCGA-ER-A19M 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A19O    TCGA-ER-A19P    TCGA-ER-A19Q    TCGA-ER-A19T    TCGA-ER-A1A1 
"FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-ER-A2NC    TCGA-ER-A2ND    TCGA-ER-A2NE    TCGA-ER-A2NF    TCGA-ER-A2NG 
   "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-ER-A2NH    TCGA-ER-A3ET    TCGA-ER-A3EV    TCGA-ER-A3PL    TCGA-ER-A42K 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-ER-A42L    TCGA-FR-A3YN    TCGA-FR-A3YO    TCGA-FR-A44A    TCGA-FR-A69P 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FS-A1YW    TCGA-FS-A1YX    TCGA-FS-A1YY    TCGA-FS-A1Z0    TCGA-FS-A1Z3 
"FC.LOW.NONSIG" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1Z4    TCGA-FS-A1Z7    TCGA-FS-A1ZA    TCGA-FS-A1ZB    TCGA-FS-A1ZC 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1ZD    TCGA-FS-A1ZE    TCGA-FS-A1ZF    TCGA-FS-A1ZG    TCGA-FS-A1ZH 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG" 
   TCGA-FS-A1ZJ    TCGA-FS-A1ZK    TCGA-FS-A1ZM    TCGA-FS-A1ZP    TCGA-FS-A1ZQ 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A1ZR    TCGA-FS-A1ZS    TCGA-FS-A1ZT    TCGA-FS-A1ZU    TCGA-FS-A1ZW 
"FC.LOW.NONSIG"    "FC.NEUTRAL" "FC.LOW.NONSIG" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-FS-A1ZY    TCGA-FS-A1ZZ    TCGA-FS-A4F0    TCGA-FS-A4F5    TCGA-FS-A4F8 
"FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-FS-A4F9    TCGA-FS-A4FB    TCGA-FS-A4FC    TCGA-FS-A4FD    TCGA-FW-A3I3 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG" 
   TCGA-FW-A3R5    TCGA-FW-A3TV    TCGA-FW-A5DY    TCGA-GF-A3OT    TCGA-GF-A4EO 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" 
   TCGA-GN-A267    TCGA-GN-A268    TCGA-GN-A26A    TCGA-GN-A26D    TCGA-GN-A4U3 
   "FC.NEUTRAL"    "FC.NEUTRAL"    "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
   TCGA-GN-A4U7    TCGA-GN-A4U9    TCGA-QB-A6FS 
   "FC.NEUTRAL" "FC.LOW.NONSIG"    "FC.NEUTRAL" 
    clus
vv   FC.LOW.NONSIG FC.NEUTRAL
  N0            38        103
  N1            14         39
  N2            10         24
  N3            14         21
[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.SIG     2   0
  FC.LOW.NONSIG  70   5
  FC.NEUTRAL    184  12
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      2    0
  FC.LOW.NONSIG   70    5
  FC.NEUTRAL     184   12
   clus
vv  FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  0           2            70        184
  1           0             5         12
[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    1  2
  FC.LOW.NONSIG 23 26
  FC.NEUTRAL    83 45
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      1    2
  FC.LOW.NONSIG   23   26
  FC.NEUTRAL      83   45
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO            1            23         83
  YES           2            26         45
[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.SIG     0   3
  FC.LOW.NONSIG   9  73
  FC.NEUTRAL     28 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      0    3
  FC.LOW.NONSIG    9   73
  FC.NEUTRAL      28  177
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO            0             9         28
  YES           3            73        177
[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.SIG     1   2
  FC.LOW.NONSIG  38  44
  FC.NEUTRAL     70 135
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      1    2
  FC.LOW.NONSIG   38   44
  FC.NEUTRAL      70  135
        clus
vv       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  FEMALE           1            38         70
  MALE             2            44        135
[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.SIG     3   0
  FC.LOW.NONSIG  70  10
  FC.NEUTRAL    180  25
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      3    0
  FC.LOW.NONSIG   70   10
  FC.NEUTRAL     180   25
     clus
vv    FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  NO            3            70        180
  YES           0            10         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"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FC.HIGH.SIG       0                         0     3
  FC.LOW.NONSIG     4                         1    77
  FC.NEUTRAL        1                         0   204
D2V13, multiclass
                           clus
vv                          FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  ASIAN                               0             4          1
  BLACK OR AFRICAN AMERICAN           0             1          0
  WHITE                               3            77        204
[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.SIG     0   2
  FC.LOW.NONSIG   1  81
  FC.NEUTRAL      2 200
[1] "tbl2"
               cls
clus            [,1] [,2]
  FC.HIGH.SIG      0    2
  FC.LOW.NONSIG    1   81
  FC.NEUTRAL       2  200
                        clus
vv                       FC.HIGH.SIG FC.LOW.NONSIG FC.NEUTRAL
  HISPANIC OR LATINO               0             1          2
  NOT HISPANIC OR LATINO           2            81        200
[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"
