[1] "ofn"        "-oTUCEC-TP"
[1] "opt"       "-OPAPOBEC"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "APOBEC"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCEC-TP/22507145/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/APOBEC_Pipelines/UCEC-TP/22555825/__DELETED__1436046:APOBEC_clinical_corr_input_22572090/APOBEC_for_clinical.correlaion.input.categorical.txt"

nPatients in clinical file=548, in cluster file=248, common to both=248
[1]   2 248
[1] "APOBEC_MUTLOAD_MINESTIMATE"
[1] 3
   0 HIGH  LOW 
 236    6    6 
   0 HIGH  LOW 
 236    6    6 
[1] "APOBEC_ENRICH"
[1] 3
FC.HIGH.ENRICH  FC.LOW.ENRICH   FC.NO.ENRICH 
            11              1            236 
FC.HIGH.ENRICH   FC.NO.ENRICH 
            11            236 
[1] "data2feature, selection=ALL"
 [1] "VITAL_STATUS"                        
 [2] "DAYS_TO_DEATH"                       
 [3] "DAYS_TO_LAST_FOLLOWUP"               
 [4] "TUMOR_TISSUE_SITE"                   
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[10] "DAYS_TO_LAST_KNOWN_ALIVE"            
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RESIDUAL_TUMOR"                      

Input Data has 13 rows and 248 columns.

[1] "Last Follow UP"
Variable 1:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 2:'DAYS_TO_DEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 3:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=209,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 4:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 10:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 248 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APOBEC_MUTLOAD_MINESTIMATE
D1V1, survival
      sevent
clus2    0   1
  0    205  31
  HIGH   5   1
  LOW    5   1
   0 HIGH  LOW 
 236    6    6 
   0 HIGH  LOW 
  31    1    1 
$`0`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G9 
       12.56        19.79         4.44        10.19        46.95        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       17.85        32.78       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        15.45        23.70        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N 
       37.51        36.79         2.63        27.42        11.51        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        16.31        35.38        10.92        37.71 
TCGA-FI-A2D2 TCGA-FI-A2EX 
       77.33         9.34 

$HIGH
TCGA-AP-A0LF TCGA-B5-A11R TCGA-BK-A0C9 TCGA-D1-A16J TCGA-E6-A1LZ TCGA-EY-A1GS 
       93.99        77.23        35.90        29.92        79.10        22.03 

$LOW
TCGA-A5-A0G5 TCGA-AJ-A23M TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-FI-A2EW TCGA-FI-A2F8 
       37.02        20.25       125.42        97.71        59.01        30.67 

    0  HIGH   LOW 
 0.56 22.03 20.25 
     0   HIGH    LOW 
185.79  93.99 125.42 
     0   HIGH    LOW 
35.560 56.565 48.015 
[1] "0.6 - 185.8 (35.6)"  "22.0 - 94.0 (56.6)"  "20.2 - 125.4 (48.0)"
D1V2, binary
      cls
clus     0   1
  0    150  86
  HIGH   3   3
  LOW    4   2
[1] "tbl2"
      cls
clus   [,1] [,2]
  0     150   86
  HIGH    3    3
  LOW     4    2
     clus
vv      0 HIGH LOW
  NO  150    3   4
  YES  86    3   2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
      vv
clus   ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID
  0                                        196                             4
  HIGH                                       4                             0
  LOW                                        0                             0
      vv
clus   SEROUS ENDOMETRIAL ADENOCARCINOMA
  0                                   36
  HIGH                                 2
  LOW                                  6
D1V3, multiclass
                                         clus
vv                                          0 HIGH LOW
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA 196    4   0
  MIXED SEROUS AND ENDOMETRIOID             4    0   0
  SEROUS ENDOMETRIAL ADENOCARCINOMA        36    2   6
[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"
      vv
clus    R0  R1  R2  RX
  0    165  10   4  18
  HIGH   3   0   2   0
  LOW    4   0   1   0
D1V4, multiclass
    clus
vv     0 HIGH LOW
  R0 165    3   4
  R1  10    0   0
  R2   4    2   1
  RX  18    0   0
[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"

Clustering(2) Variable = APOBEC_ENRICH
D2V1, survival
                sevent
clus2              0   1
  FC.HIGH.ENRICH   9   2
  FC.NO.ENRICH   205  31
FC.HIGH.ENRICH   FC.NO.ENRICH 
            11            236 
FC.HIGH.ENRICH   FC.NO.ENRICH 
             2             31 
$FC.HIGH.ENRICH
TCGA-AP-A0LF TCGA-AJ-A23M TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-B5-A11R TCGA-BK-A0C9 
       93.99        20.25       125.42        97.71        77.23        35.90 
TCGA-D1-A16J TCGA-E6-A1LZ TCGA-EY-A1GS TCGA-FI-A2EW TCGA-FI-A2F8 
       29.92        79.10        22.03        59.01        30.67 

$FC.NO.ENRICH
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       88.18        60.53       110.63        57.80        67.66        36.39 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A212 TCGA-A5-A0G3 TCGA-A5-A0G9 
       12.56        19.79         4.44        10.19        46.95        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       17.85        32.78       112.54       105.37        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VO TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       28.77        42.35        15.95       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DQ TCGA-AX-A05S TCGA-AX-A05T 
       80.78        49.22        25.08        46.78        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       79.46        49.87        27.39        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H5 
       37.78        40.11        77.39        34.65        25.51        71.24 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        86.37        55.30        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        44.78        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
       32.09        73.28        16.73        19.56        19.50        19.59 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0LW 
       18.41        17.36        16.57        50.89        11.87        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ 
       74.63        41.52        48.56        23.47        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CA TCGA-BK-A0CB 
       14.01        15.45        15.45        23.70        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       35.08        31.00        24.99        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        86.93        72.72        73.25        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N 
       37.51        36.79         2.63        27.42        11.51        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-DI-A0WH TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       13.22        18.25        16.31        35.38        10.92        37.71 
TCGA-FI-A2D2 TCGA-FI-A2EX 
       77.33         9.34 

FC.HIGH.ENRICH   FC.NO.ENRICH 
         20.25           0.56 
FC.HIGH.ENRICH   FC.NO.ENRICH 
        125.42         185.79 
FC.HIGH.ENRICH   FC.NO.ENRICH 
         59.01          35.56 
[1] "20.2 - 125.4 (59.0)" "0.6 - 185.8 (35.6)" 
[1] "hr=" "1"  
D2V2, binary
                cls
clus               0   1
  FC.HIGH.ENRICH   7   4
  FC.NO.ENRICH   150  86
[1] "tbl2"
                cls
clus             [,1] [,2]
  FC.HIGH.ENRICH    7    4
  FC.NO.ENRICH    150   86
     clus
vv    FC.HIGH.ENRICH FC.NO.ENRICH
  NO               7          150
  YES              4           86
[1] 2 2
[1] FALSE
                vv
clus             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  FC.HIGH.ENRICH                                       4
  FC.NO.ENRICH                                       196
                vv
clus             MIXED SEROUS AND ENDOMETRIOID
  FC.HIGH.ENRICH                             0
  FC.NO.ENRICH                               4
                vv
clus             SEROUS ENDOMETRIAL ADENOCARCINOMA
  FC.HIGH.ENRICH                                 7
  FC.NO.ENRICH                                  36
D2V3, multiclass
                                         clus
vv                                        FC.HIGH.ENRICH FC.NO.ENRICH
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              4          196
  MIXED SEROUS AND ENDOMETRIOID                        0            4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    7           36
[1] 3 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              R0  R1  R2  RX
  FC.HIGH.ENRICH   6   0   3   0
  FC.NO.ENRICH   165  10   4  18
D2V4, multiclass
    clus
vv   FC.HIGH.ENRICH FC.NO.ENRICH
  R0              6          165
  R1              0           10
  R2              3            4
  RX              0           18
[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"
