[1] "ofn"        "-oTBRCA-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/20125499/BRCA-TP.mergedcluster.txt"

nPatients in clinical file=1098, in cluster file=1098, common to both=1098
[1]   12 1098
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
102 156 118  92  58 
  1   2   3   4   5 
102 156 118  92  58 
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
275 407  98 257  43 
  1   2   3   4   5 
275 407  98 257  43 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5   6 
147 101 216 123 137  59 
  1   2   3   4   5   6 
147 101 216 123 137  59 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
156 126 128 
  1   2   3 
156 126 128 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 64  49  93  54 118  32 
  1   2   3   4   5   6 
 64  49  93  54 118  32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
567 311 215 
  1   2   3 
567 311 215 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
294 166  91 294 188  60 
  1   2   3   4   5   6 
294 166  91 294 188  60 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
309 214 274 281 
  1   2   3   4 
309 214 274 281 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
300 155 248 141  98 136 
  1   2   3   4   5   6 
300 155 248 141  98 136 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
182 140 102 111 133 
  1   2   3   4   5 
182 140 102 111 133 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
309 249 110 
  1   2   3 
309 249 110 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 1098 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=144,	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=764,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 1098 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=65, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
283 634 137  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
283 634 137  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
283 634 137  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
283 634 137  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
517 364 120  77 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
517 364 120  77 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
517 364 120  77 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
517 364 120  77 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=31, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 17  3
  subtype2 36  3
  subtype3 96 20
  subtype4 86 14
  subtype5 94 14
  subtype6 55 16
  subtype7 15  4
  subtype8 31  8
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      20       39      116      100      108       71       19       39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       3        3       20       14       14       16        4        8 
$subtype1
TCGA-A1-A0SD TCGA-A1-A0SH TCGA-A1-A0SM TCGA-A2-A0SV TCGA-A8-A06P TCGA-A8-A07G 
       14.37        47.24         7.96        27.12        13.02        18.97 
TCGA-A8-A07I TCGA-A8-A08Z TCGA-A8-A097 TCGA-AN-A03X TCGA-AN-A0AS TCGA-AN-A0XN 
       14.01        40.01        12.00         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-BH-A0DZ TCGA-BH-A0H6 TCGA-BH-A18J TCGA-BH-A1EO TCGA-C8-A12O 
        5.59        16.27        24.56        20.12        91.99        12.66 
TCGA-D8-A141 TCGA-E2-A153 
       20.58        23.24 

$subtype2
TCGA-A1-A0SE TCGA-A2-A0CP TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES 
       43.43        92.48        98.99        53.13        80.28        72.00 
TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0T7 TCGA-A2-A0YL TCGA-A8-A08O TCGA-A8-A09A 
       24.72        54.64        20.75        48.46        31.00         9.99 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0JA TCGA-AO-A0JB 
       13.02        21.04        80.28        61.35        21.53        50.70 
TCGA-AO-A12C TCGA-AO-A12E TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AU TCGA-B6-A0IE 
       65.56        57.30        96.00        86.07        94.29        65.72 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0DG 
      140.48       157.41       113.79        63.09        37.74        23.44 
TCGA-BH-A0DI TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-C8-A132 TCGA-C8-A1HI TCGA-E2-A14Q 
       29.98        46.19        24.43         1.87        11.28        38.24 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A1B1 
       20.71        12.92        87.22 

$subtype3
TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68       121.94        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0T3 
      107.93        25.22        74.40        35.05        34.29        49.84 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F 
       21.67        23.77        38.30        30.61        37.45        25.15 
TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L 
       13.02        29.03        31.00         1.02         9.01        32.05 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08F 
       10.98         9.99        45.07        36.95        13.02        33.01 
TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
       19.96        33.01        50.04        49.05        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AK 
       25.02         8.98         0.23         0.62         2.96         7.36 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XT 
        6.44         5.65         0.36         0.33         0.33         0.33 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J7 
       95.70        68.75        47.87        29.13        21.40        20.32 
TCGA-AO-A0JI TCGA-AO-A126 TCGA-AO-A12H TCGA-AQ-A04H TCGA-AR-A0TQ TCGA-AR-A0TV 
       50.24       108.72        40.57        24.79        98.33        75.22 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-B6-A0IM TCGA-B6-A0IN 
       98.93        55.86       107.24        83.87       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV 
      165.76        68.45        81.17        78.02       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0X5 TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0B8 TCGA-BH-A0C7 
       18.35        68.94        62.93        39.16        51.58        90.97 
TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0E2 TCGA-BH-A0GZ TCGA-BH-A0H0 
       45.83        38.01        13.91        14.30        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L 
       37.78        23.08        26.50        51.32        27.25        26.66 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A12W 
       37.74        37.55       113.82        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HG TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 
       12.66        48.53        11.34        12.95        13.25        43.00 
TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       83.54        46.59        40.41        44.68        33.17        75.98 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       32.02        21.04        23.34        21.63        50.79        56.94 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        51.39 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       31.79        28.01        19.20        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST 
       87.25        24.79        55.00        67.33        33.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O 
       35.31        35.67        31.73        20.19        33.99         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-AN-A04D TCGA-AN-A0AL 
        8.98        24.99         0.99        43.00         1.71         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX 
        0.16         0.33         0.33         7.96         7.59         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL 
        0.53         0.33        58.95        52.18        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TP 
      115.27       106.78       108.03        48.36        26.93       140.55 
TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       84.10        23.31        65.36       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 
      101.00        99.32        17.23        33.73       143.38        32.58 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX 
      233.62       140.88       255.68        89.46       282.90        21.47 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
      245.10        59.84        39.55        51.68        61.51        74.89 
TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA 
       77.95        78.28         4.41         9.63         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1F0 TCGA-C8-A12L 
        4.90        90.84        55.63        51.16        25.81        11.93 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A143 
       12.66        13.51        12.59        56.81        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       19.20        47.15        38.60        31.96        69.34        63.62 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B5 
       14.79        25.05        76.57        32.35 

$subtype5
TCGA-A2-A04N TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EV 
      143.15        88.60        77.19        61.58       101.72        31.82 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A7-A0CH 
       17.46        32.55        25.28        50.47        49.48        35.47 
TCGA-A7-A0DB TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07S TCGA-A8-A08A 
       33.11        53.06        26.01        18.97         7.99         0.99 
TCGA-A8-A08C TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       28.96        33.01       112.08        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 
       12.00         1.02        19.04        15.02        12.00        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0FK 
       27.02        17.03        38.04         0.33         0.33         7.00 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A0J8 TCGA-AO-A125 
       12.33         0.30         0.33         5.33        22.36        99.25 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12G TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AP 
       90.58        98.27        41.62         5.26       103.86        93.90 
TCGA-AR-A1AS TCGA-AR-A1AW TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       37.81        86.53       281.29       275.87       129.57        50.70 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WZ 
      129.07       234.28       263.28       162.05       102.77       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
      129.70        28.27        70.22        37.22        32.02        18.21 
TCGA-BH-A0BJ TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0DO 
       21.70        74.14        53.95        45.57        49.94        17.26 
TCGA-BH-A0DP TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.65        38.47        15.68        44.81        32.58        24.49 
TCGA-BH-A0HA TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        23.90        20.38         2.50        13.61        36.85 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18S 
       23.93        24.95        42.35        35.93        72.56        66.05 
TCGA-BH-A1ET TCGA-C8-A12N TCGA-D8-A146 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       82.85        11.77        21.14        37.51        28.44        28.87 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I 
       19.43        23.87        22.82        17.29        18.21        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B4 TCGA-E2-A1BD 
       53.92         9.04        20.58        19.56        33.01        37.25 

$subtype6
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EY TCGA-A2-A0SW 
      101.98        55.43        56.81        34.55        63.29        44.88 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A076 
       17.13        21.90         1.02        17.98        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A092 
       43.00        15.06        38.01        37.05         9.99        30.97 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X TCGA-AN-A04C TCGA-AN-A0FT 
       45.07         1.02         0.99        14.01         1.78         7.04 
TCGA-AN-A0FV TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM 
        0.33        66.77        32.78        72.00        76.77        71.80 
TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 TCGA-AR-A1AT TCGA-B6-A0I8 
       64.04       130.09        64.83       134.14        41.82        24.62 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH TCGA-B6-A0RS TCGA-BH-A0AW 
       12.13       146.50        18.77       212.25       100.70        20.45 
TCGA-BH-A0B7 TCGA-BH-A0BR TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0EE TCGA-BH-A0GY 
       84.13        76.60        44.02         2.56        31.00        30.35 
TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U 
       41.00        12.89        50.79        30.28         7.36        51.39 
TCGA-BH-A1EV TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A135 
       12.00        11.77        12.66        12.56         3.16        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HL TCGA-D8-A13Z TCGA-E2-A107 
        4.11         4.08        10.92        10.42        20.88        34.42 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A1B0 
       40.11        40.96        34.26        69.96        53.62 

$subtype7
TCGA-A2-A0CL TCGA-A2-A0EQ TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A0A7 TCGA-AN-A0AJ 
       99.12        79.76        12.00        31.00         0.99         9.96 
TCGA-AO-A03O TCGA-AO-A0JC TCGA-AR-A0TT TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0WS 
       81.63        50.86       109.02        61.28        86.43        97.48 
TCGA-BH-A0BF TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0H5 TCGA-BH-A0W7 TCGA-C8-A1HM 
       43.53        49.05        41.75        53.26        44.81        12.33 
TCGA-E2-A14Z 
       18.51 

$subtype8
TCGA-A2-A0EN TCGA-A2-A0EW TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0YK 
       89.36        61.94        44.28        20.52        18.90        19.33 
TCGA-A7-A0CG TCGA-A8-A07E TCGA-A8-A07J TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
       34.29        19.99        12.00         7.17         6.90         5.36 
TCGA-AN-A0XS TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
        0.33        26.04        53.03        65.10        26.24        62.04 
TCGA-AR-A1AL TCGA-B6-A0IH TCGA-B6-A0X7 TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0BM 
       97.68       112.37        58.88        25.55        81.44        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DQ TCGA-BH-A0DX 
       72.23        75.48        89.06        77.98         3.22        70.88 
TCGA-BH-A0HK TCGA-BH-A18F TCGA-BH-A1EU TCGA-BH-A1EW TCGA-D8-A145 TCGA-E2-A108 
        5.85        32.91        42.28        55.69        13.48        27.52 
TCGA-E2-A15M TCGA-E2-A1B6 TCGA-E2-A1BC 
       11.05        28.50        16.47 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.33     1.87     0.23     0.16     0.30     0.33     0.99     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   91.99   157.41   188.68   282.90   281.29   212.25   109.02   112.37 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  15.320   50.700   33.120   33.875   32.565   32.780   49.050   32.910 
[1] "0.3 - 92.0 (15.3)"  "1.9 - 157.4 (50.7)" "0.2 - 188.7 (33.1)"
[4] "0.2 - 282.9 (33.9)" "0.3 - 281.3 (32.6)" "0.3 - 212.2 (32.8)"
[7] "1.0 - 109.0 (49.0)" "0.3 - 112.4 (32.9)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1        0        0        0         8         3          5
  subtype2       2        2        0        0        12        10          8
  subtype3       8        7        3        0        35        35         20
  subtype4       9        9        0        0        45        20          9
  subtype5      16       12        0        1        42        15         10
  subtype6       4        2        0        0        21        19         15
  subtype7       4        1        0        0         6         4          4
  subtype8       6        3        0        0        14         6          6
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          1          0        2         0       0
  subtype2          0          2        1         1       1
  subtype3          6          3        1         0       3
  subtype4          1          4        2         0       1
  subtype5          5          2        3         0       4
  subtype6          2          6        3         0       1
  subtype7          0          0        0         0       1
  subtype8          0          2        1         0       2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        2        8        9       16        4        4
  STAGE IA          0        2        7        9       12        2        1
  STAGE IB          0        0        3        0        0        0        0
  STAGE II          0        0        0        0        1        0        0
  STAGE IIA         8       12       35       45       42       21        6
  STAGE IIB         3       10       35       20       15       19        4
  STAGE IIIA        5        8       20        9       10       15        4
  STAGE IIIB        1        0        6        1        5        2        0
  STAGE IIIC        0        2        3        4        2        6        0
  STAGE IV          2        1        1        2        3        3        0
  STAGE TIS         0        1        0        0        0        0        0
  STAGE X           0        1        3        1        4        1        1
            clus
vv           subtype8
  STAGE I           6
  STAGE IA          3
  STAGE IB          0
  STAGE II          0
  STAGE IIA        14
  STAGE IIB         6
  STAGE IIIA        6
  STAGE IIIB        0
  STAGE IIIC        2
  STAGE IV          1
  STAGE TIS         0
  STAGE X           2
[1] 12  8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  5 14  0  2
  subtype2  8 21  9  0
  subtype3 25 75 14  6
  subtype4 23 67  8  2
  subtype5 40 55  9  6
  subtype6 11 49 12  2
  subtype7  7 10  3  0
  subtype8 13 21  4  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        5        8       25       23       40       11        7       13
  T2       14       21       75       67       55       49       10       21
  T3        0        9       14        8        9       12        3        4
  T4        2        0        6        2        6        2        0        2
[1] 4 8
[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
  subtype1  6  6  7  1
  subtype2 14 16  5  3
  subtype3 49 50 14  4
  subtype4 64 25  7  5
  subtype5 66 31  7  5
  subtype6 24 26 14  8
  subtype7 11  5  3  0
  subtype8 21 12  3  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        6       14       49       64       66       24       11       21
  N1        6       16       50       25       31       26        5       12
  N2        7        5       14        7        7       14        3        3
  N3        1        3        4        5        5        8        0        3
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1  19   2
  subtype2  37   1
  subtype3 115   2
  subtype4  97   3
  subtype5 101   3
  subtype6  70   3
  subtype7  19   0
  subtype8  37   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    2
  subtype2   37    1
  subtype3  115    2
  subtype4   97    3
  subtype5  101    3
  subtype6   70    3
  subtype7   19    0
  subtype8   37    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       19       37      115       97      101       70       19       37
  1        2        1        2        3        3        3        0        1
[1] 2 8
[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
  subtype1  20   1
  subtype2  39   0
  subtype3 117   4
  subtype4 101   0
  subtype5 110   0
  subtype6  74   0
  subtype7  19   1
  subtype8  40   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   39    0
  subtype3  117    4
  subtype4  101    0
  subtype5  110    0
  subtype6   74    0
  subtype7   19    1
  subtype8   40    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       20       39      117      101      110       74       19
  MALE          1        0        4        0        0        0        1
        clus
vv       subtype8
  FEMALE       40
  MALE          0
[1] 2 8
[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
  subtype1  7  6
  subtype2 15 19
  subtype3 55 49
  subtype4 36 51
  subtype5 45 46
  subtype6 27 32
  subtype7  6 10
  subtype8 12 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    6
  subtype2   15   19
  subtype3   55   49
  subtype4   36   51
  subtype5   45   46
  subtype6   27   32
  subtype7    6   10
  subtype8   12   23
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         7       15       55       36       45       27        6       12
  YES        6       19       49       51       46       32       10       23
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            20                              0
  subtype2                            28                              8
  subtype3                           113                              1
  subtype4                            92                              1
  subtype5                            85                             14
  subtype6                            67                              5
  subtype7                            19                              1
  subtype8                            22                             13
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                3
  subtype3                   0                                0
  subtype4                   1                                0
  subtype5                   0                                5
  subtype6                   0                                0
  subtype7                   0                                0
  subtype8                   0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              0
  subtype3                  1              6
  subtype4                  0              6
  subtype5                  1              5
  subtype6                  0              2
  subtype7                  0              0
  subtype8                  0              2
D1V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          20       28      113       92       85
  INFILTRATING LOBULAR CARCINOMA          0        8        1        1       14
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        3        0        0        5
  MUCINOUS CARCINOMA                      0        0        1        0        1
  OTHER  SPECIFY                          1        0        6        6        5
                                  clus
vv                                 subtype6 subtype7 subtype8
  INFILTRATING DUCTAL CARCINOMA          67       19       22
  INFILTRATING LOBULAR CARCINOMA          5        1       13
  MEDULLARY CARCINOMA                     0        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        0        3
  MUCINOUS CARCINOMA                      0        0        0
  OTHER  SPECIFY                          2        0        2
[1] 6 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         0
  subtype2                                0     4                         3
  subtype3                                0    10                        12
  subtype4                                0     6                        12
  subtype5                                0     2                         5
  subtype6                                1     9                         2
  subtype7                                0     1                         5
  subtype8                                0     0                         1
          vv
clus       WHITE
  subtype1    14
  subtype2    28
  subtype3    74
  subtype4    75
  subtype5    81
  subtype6    43
  subtype7    11
  subtype8    35
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   2        4       10        6        2
  BLACK OR AFRICAN AMERICAN               0        3       12       12        5
  WHITE                                  14       28       74       75       81
                                  clus
vv                                 subtype6 subtype7 subtype8
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   9        1        0
  BLACK OR AFRICAN AMERICAN               2        5        1
  WHITE                                  43       11       35
[1] 4 8
[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
  subtype1  0 14
  subtype2  1 32
  subtype3  0 83
  subtype4  1 83
  subtype5  2 70
  subtype6  2 46
  subtype7  1 14
  subtype8  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   14
  subtype2    1   32
  subtype3    0   83
  subtype4    1   83
  subtype5    2   70
  subtype6    2   46
  subtype7    1   14
  subtype8    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        1        2        2
  NOT HISPANIC OR LATINO       14       32       83       83       70       46
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            1        0
  NOT HISPANIC OR LATINO       14       30
[1] 2 8
[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 = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1  81  17
  subtype2 133  22
  subtype3  91  22
  subtype4  78  13
  subtype5  47   8
subtype1 subtype2 subtype3 subtype4 subtype5 
      98      155      113       91       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      17       22       22       13        8 
$subtype1
TCGA-A1-A0SD TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       14.37       121.94        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0YH TCGA-A2-A0YT 
      107.93        25.22        74.40        34.29        21.67        23.77 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A8-A06T TCGA-A8-A06X 
       38.30        30.61        37.45        25.15        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A085 
       26.01         1.02         9.01        32.05        10.98        36.95 
TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09C 
       13.02        33.01        19.96        33.01        33.01         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A0A9 
       50.04        49.05        29.98        33.07         8.98        27.02 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FY 
        0.33         0.23         0.62         7.36         6.44         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI TCGA-AQ-A04H 
        0.33         0.33        95.70        21.40        50.24        24.79 
TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 
       98.33        75.22        98.93        55.86       107.24        83.87 
TCGA-B6-A0IB TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL 
      129.57       127.33       165.76        68.45       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X5 TCGA-BH-A0B4 
       78.02       188.68        79.63        18.35        68.94        39.16 
TCGA-BH-A0B8 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0E2 TCGA-BH-A0GZ 
       51.58        90.97        45.83        38.01        14.30        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L 
       15.16        37.78        26.50        51.32        27.25        26.66 
TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HL 
      113.82        11.77        12.66        12.66        48.53        10.42 
TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14S 
       12.95        13.25        43.00        46.59        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       75.98        32.02        21.04        21.63        50.79        56.94 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        51.39 

$subtype2
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A0CL TCGA-A2-A0CP 
       43.43        47.24        13.68       143.15        99.12        92.48 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ES 
       98.99        53.13        61.58        89.36        80.28        72.00 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T3 
       31.82        61.94        24.72        54.64        44.28        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YK 
       20.52        17.46        18.90        20.75        25.28        19.33 
TCGA-A2-A0YL TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A8-A07E TCGA-A8-A07J TCGA-A8-A08C 
       48.46        34.29        33.11        19.99        12.00        28.96 
TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A09A TCGA-A8-A0A1 TCGA-A8-A0A2 
       31.00       112.08        40.01         9.99        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
       13.02        21.04        17.03         0.33         0.33         2.96 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XV 
        7.17         6.90         0.36         5.36         0.33         5.33 
TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J9 
       61.35        68.75        47.87        29.13        26.04        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       21.53        50.70        50.86        65.10        26.24        62.04 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AR-A0TT 
      108.72        90.58        65.56        57.30        41.62       109.02 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AU 
      103.86        97.68        96.00        86.07        93.90        94.29 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IH 
       61.28        86.43       281.29       275.87        65.72       112.37 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WS 
       84.59       129.07       263.28       140.48       157.41        97.48 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      113.79       129.70        58.88        62.93        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       81.44        70.22        37.22        32.02        18.21        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BT 
       21.70        61.68        72.23        75.48        74.14        45.57 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       89.06        77.98        23.44        29.98        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E1 
       15.65         3.22         2.56        38.47        70.88        15.68 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HF 
       46.19        32.58        24.43        53.26        52.96        23.90 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
        5.85        13.61        36.85        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       32.91        35.93        72.56        91.99        82.85        42.28 
TCGA-BH-A1EW TCGA-C8-A132 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-D8-A141 TCGA-D8-A145 
       55.69         1.87        11.34        11.28        20.58        13.48 
TCGA-D8-A146 TCGA-E2-A106 TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14Z 
       21.14        83.54        27.52        28.87        38.24        18.51 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        20.71        12.92        55.63        53.92 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC 
       11.05        19.56        87.22        28.50        16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0CY 
       31.79         7.96       101.98        55.43        56.81        55.00 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T1 
       34.55        79.76        63.29        27.12        44.88        17.13 
TCGA-A2-A0YG TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 
       21.90        13.02         1.02        17.98        29.03        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07W 
       53.98        43.00        18.97        18.97        14.01         9.99 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
       15.06        38.01        12.00        37.05         9.99        31.00 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N 
       43.00        30.97        41.98        12.00        45.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04C TCGA-AN-A0AJ 
       25.02         0.99        14.01         0.99         1.78         9.96 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        0.16         0.33         7.04         0.33         0.33        12.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0JD 
        5.59        80.28        66.77        81.63        32.78        72.00 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 
       76.77        71.80        64.04       130.09        64.83       134.14 
TCGA-AR-A1AT TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH 
       41.82        24.62        12.13       146.50        18.77       212.25 
TCGA-B6-A0RO TCGA-B6-A0RS TCGA-BH-A0AW TCGA-BH-A0B1 TCGA-BH-A0B7 TCGA-BH-A0BR 
      162.05       100.70        20.45        37.74        84.13        76.60 
TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0EE 
       53.95        49.05        41.75        44.02        16.27        31.00 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J 
       30.35        23.08        41.00        12.89        50.79        20.12 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EV TCGA-C8-A12L 
       30.28        37.55         7.36        51.39        12.00        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 
       12.66        11.77        12.66        12.66        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM 
       13.51        12.92         4.11         4.08        10.92        12.33 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14P 
       56.81        20.88        14.17        34.42        40.11        40.96 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1B0 
       34.26        69.96        25.05        23.34        53.62 

$subtype4
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       28.01        19.20        18.02        78.41        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 
       24.79        67.33        33.76        99.19        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE TCGA-A7-A0DA 
        8.38        18.21        18.61        31.73        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
       31.73        20.19        33.99         9.99         8.98        24.99 
TCGA-A8-A08R TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        0.99         1.71         7.46         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 
        7.59         0.33         0.53         0.33        58.95        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F 
       37.48        55.33       115.27       106.78       108.03        48.36 
TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       26.93       140.55        84.10        23.31        65.36       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
      125.16       108.36       101.00        99.32        17.23        33.73 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT 
      143.38        32.58       233.62       140.88       255.68        89.46 
TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 
      282.90        21.47       245.10        59.84        39.55        51.68 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 
       61.51        74.89        77.95        78.28         4.41         9.63 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V 
        5.59        23.05         4.90        90.84        55.63        51.16 
TCGA-BH-A1F0 TCGA-C8-A12V TCGA-C8-A134 TCGA-D8-A142 TCGA-D8-A147 TCGA-E2-A14N 
       25.81        12.66        12.59        13.97        19.20        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A1AZ 
       38.60        31.96        69.34        63.62        14.79        76.57 
TCGA-E2-A1B5 
       32.35 

$subtype5
TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0EM TCGA-A2-A0ET TCGA-A2-A0YC TCGA-A2-A0YF 
       88.60        77.19       101.72        35.05        32.55        50.47 
TCGA-A2-A0YI TCGA-A7-A0CH TCGA-A8-A06P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A08A 
       49.48        35.47        13.02         7.99        45.07         0.99 
TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0AD 
       17.95         9.99        12.00        19.04        15.02        38.04 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A0J8 
        5.65         7.00         0.30         0.33        20.32        22.36 
TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AW 
       99.25        98.27        40.57         5.26        37.81        86.53 
TCGA-B6-A0IC TCGA-B6-A0RP TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-BH-A0BV TCGA-BH-A0E7 
       50.70       102.77       206.86        28.27        49.94        44.81 
TCGA-BH-A0EB TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0W3 TCGA-BH-A18N 
       24.49        24.56        20.38         2.50        23.93        37.74 
TCGA-BH-A18S TCGA-C8-A12N TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 
       66.05        11.77        40.41        37.51        28.44        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15G TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A1B4 
       19.43        23.87        18.21         9.04        20.58        33.01 
TCGA-E2-A1BD 
       37.25 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.33     0.16     0.33     0.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
  234.28   281.29   212.25   282.90   206.86 
subtype1 subtype2 subtype3 subtype4 subtype5 
   33.04    42.28    27.12    35.31    28.27 
[1] "0.2 - 234.3 (33.0)" "0.3 - 281.3 (42.3)" "0.2 - 212.2 (27.1)"
[4] "0.3 - 282.9 (35.3)" "0.3 - 206.9 (28.3)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       6        6        1        0        32        30         16
  subtype2      21       13        2        0        56        24         23
  subtype3       6        4        0        0        36        27         24
  subtype4       9        8        0        0        40        19          8
  subtype5       8        5        0        1        19        12          6
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          5          2        1         0       3
  subtype2          1          6        3         1       5
  subtype3          5          8        6         0       1
  subtype4          1          3        2         0       1
  subtype5          3          0        1         0       3
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       21        6        9        8
  STAGE IA          6       13        4        8        5
  STAGE IB          1        2        0        0        0
  STAGE II          0        0        0        0        1
  STAGE IIA        32       56       36       40       19
  STAGE IIB        30       24       27       19       12
  STAGE IIIA       16       23       24        8        6
  STAGE IIIB        5        1        5        1        3
  STAGE IIIC        2        6        8        3        0
  STAGE IV          1        3        6        2        1
  STAGE TIS         0        1        0        0        0
  STAGE X           3        5        1        1        3
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 19 63 14  5
  subtype2 54 79 19  3
  subtype3 18 78 15  7
  subtype4 22 60  8  1
  subtype5 19 32  3  4
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       19       54       18       22       19
  T2       63       79       78       60       32
  T3       14       19       15        8        3
  T4        5        3        7        1        4
[1] 4 5
[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
  subtype1 44 43  9  4
  subtype2 81 47 15  9
  subtype3 41 39 25 10
  subtype4 58 24  6  4
  subtype5 31 18  5  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       44       81       41       58       31
  N1       43       47       39       24       18
  N2        9       15       25        6        5
  N3        4        9       10        4        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1  96   2
  subtype2 146   3
  subtype3 111   6
  subtype4  88   3
  subtype5  54   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96    2
  subtype2  146    3
  subtype3  111    6
  subtype4   88    3
  subtype5   54    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       96      146      111       88       54
  1        2        3        6        3        1
[1] 2 5
[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
  subtype1  98   4
  subtype2 155   1
  subtype3 117   1
  subtype4  92   0
  subtype5  58   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98    4
  subtype2  155    1
  subtype3  117    1
  subtype4   92    0
  subtype5   58    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       98      155      117       92       58
  MALE          4        1        1        0        0
[1] 2 5
[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
  subtype1 44 43
  subtype2 63 66
  subtype3 47 47
  subtype4 30 49
  subtype5 19 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   43
  subtype2   63   66
  subtype3   47   47
  subtype4   30   49
  subtype5   19   31
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        44       63       47       30       19
  YES       43       66       47       49       31
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            97                              1
  subtype2                           111                             31
  subtype3                           110                              6
  subtype4                            84                              1
  subtype5                            44                              4
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                7
  subtype3                   0                                0
  subtype4                   1                                0
  subtype5                   0                                4
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  1              3
  subtype2                  0              7
  subtype3                  0              2
  subtype4                  0              5
  subtype5                  1              5
D2V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          97      111      110       84       44
  INFILTRATING LOBULAR CARCINOMA          1       31        6        1        4
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        7        0        0        4
  MUCINOUS CARCINOMA                      1        0        0        0        1
  OTHER  SPECIFY                          3        7        2        5        5
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        10
  subtype2                                0     6                         8
  subtype3                                1    16                         4
  subtype4                                0     3                        12
  subtype5                                0     2                         6
          vv
clus       WHITE
  subtype1    60
  subtype2   128
  subtype3    65
  subtype4    70
  subtype5    38
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   7        6       16        3        2
  BLACK OR AFRICAN AMERICAN              10        8        4       12        6
  WHITE                                  60      128       65       70       38
[1] 4 5
[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
  subtype1   0  66
  subtype2   3 119
  subtype3   2  74
  subtype4   1  75
  subtype5   1  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    3  119
  subtype3    2   74
  subtype4    1   75
  subtype5    1   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        3        2        1        1
  NOT HISPANIC OR LATINO       66      119       74       75       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 234  37
  subtype2 349  50
  subtype3  84  14
  subtype4 217  37
  subtype5  33   9
subtype1 subtype2 subtype3 subtype4 subtype5 
     271      399       98      254       42 
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       50       14       37        9 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SJ 
      129.14       131.67        42.81         9.96        14.37        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CT 
        7.96        39.32        18.21       121.94        55.43        75.25 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       25.22        80.28        74.40        35.05        34.29        31.82 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YG 
       27.12        44.88        49.84        20.52        20.75        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25E TCGA-A7-A0CD 
       23.77        17.36        60.72        42.44       105.34        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       30.61        29.79        25.15        20.61        22.32        10.59 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       14.93        13.74        17.92        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       53.06        29.03         1.02        53.98         9.01        43.00 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 
       18.97        14.01        32.05        10.98         9.99        36.95 
TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       13.02        33.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E 
       31.00        33.01        12.00         9.99         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A4 
       45.07        29.98        33.07         8.98         0.99        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3QQ 
       21.04        27.02         5.72        99.35        26.04        24.13 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A03X 
       29.26        16.80        11.44         8.22        20.19         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FV 
        0.33         0.23         0.62         2.96         9.96         0.33 
TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P 
        0.36         5.36         5.59        80.28        81.63        95.70 
TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JG 
       47.87        32.78        21.40        72.00        76.77        26.24 
TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT 
       50.24        71.80        57.30        61.87         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TZ 
       24.79         5.65        15.62        32.91        98.33       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A24L TCGA-AR-A24R 
       83.87       134.14       103.86        93.90        94.22       112.77 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK 
      105.30        98.66        89.00        85.64        71.05        54.21 
TCGA-AR-A2LL TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RO 
       66.15        12.13       146.50        68.45        81.17       162.05 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B4 
       79.63       113.79       139.17        68.12        62.93        39.16 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DI TCGA-BH-A0DL 
       32.02        18.21        90.97        45.83        29.98        78.28 
TCGA-BH-A0DQ TCGA-BH-A0DZ TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HW 
        3.22        16.27        14.30        24.43        23.08        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N 
       27.25        50.79        23.93        35.93        26.66        37.74 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EW 
       37.55        66.05        51.39        67.50       113.82        55.69 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A42T TCGA-BH-A5J0 
       31.53        24.62        45.63        28.14        10.52        23.51 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HL 
        1.87         4.11         4.08        11.34        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 
       12.95        12.33         8.28         9.67        24.56        12.95 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1J9 TCGA-D8-A1JC 
       12.49        19.46        56.81        13.25        17.49        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.15        18.90        18.97        13.32        23.90        27.58 
TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 
       15.22        16.31        16.64        16.54        15.52        14.14 
TCGA-D8-A27G TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 
       13.45         4.80        10.09        12.26        43.00        46.59 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       44.68        40.96        33.17        75.98        34.26        32.02 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15O TCGA-E2-A15S 
       69.96        23.34        20.71        12.92        50.79        14.07 
TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1LA TCGA-E2-A56Z TCGA-E2-A9RU 
       51.39        77.65        70.36        24.59         8.28        17.69 
TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R6 
       36.56        35.24         9.86        24.82        34.95        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22D 
       48.23        46.65         6.58        21.27        42.25        41.03 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW 
       38.99        12.33        29.72        25.81        26.40        12.20 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 
       16.57        15.68        28.77        29.85        40.41        23.11 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A6SA TCGA-GM-A2D9 
       18.90        13.94        52.73        22.09        16.77        59.57 
TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A66O TCGA-PE-A5DC 
       15.32         2.63        12.36        22.32        17.36        47.01 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-UL-AAZ6 
        0.16        18.81        18.48        21.07        13.94        17.03 
TCGA-Z7-A8R6 
      107.05 

$subtype2
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SF 
       40.14        11.44        48.56        48.36         8.52        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04W 
       14.27        47.24       143.15        78.41        63.12       101.98 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        99.12       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES 
      107.93        61.58       101.72        89.36       118.45        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 
       61.94        24.72        99.19        54.64        44.28        17.13 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       17.46        18.90        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 
       49.48        19.33        48.46        22.45        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       52.47       107.70        17.19        10.59        36.23        39.65 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       32.75        56.28        50.37        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       26.96        34.29        35.47        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       24.26        23.80        11.34        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A07E TCGA-A8-A07J 
       11.97        10.72        11.05        13.02        19.99        12.00 
TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A09T 
        7.99         0.99       112.08        40.01        41.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
       15.02        14.01         0.99        38.04        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP 
       74.14        19.33        14.66        32.45        16.31        22.19 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       25.05        14.99        19.79        15.48        23.24        24.79 
TCGA-AC-A5EI TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS 
       14.53        18.67        12.26         0.03         1.32         2.30 
TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.65         7.17         6.90         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JC 
        5.33        58.95        26.04        22.36        21.53        50.86 
TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B 
       65.10        62.04        99.25       108.72       106.78        98.27 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TX 
       40.57        14.73        32.52        19.20        84.10        64.83 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      101.00        97.68        98.33        96.00        86.07        99.32 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N 
       37.81        94.29        86.53        86.43       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A252 
      118.59         2.76       105.27        32.58        98.76        93.30 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0IC 
       40.54        33.30        38.96        10.59       281.29        50.70 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      127.33        84.59       129.07       234.28        78.02       263.28 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WZ 
      140.48        89.46       157.41        97.48       188.68       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A3ZX 
      129.70        28.27        68.94        58.88        73.51        37.87 
TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B7 
       85.35        71.15        63.09        81.44        40.83        84.13 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C3 
       61.68        72.23        74.14        53.95        49.05        89.06 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DT 
       77.98        23.44        38.01        13.91        17.26        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       67.86        70.88        15.68        44.81        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HI 
       31.00        37.78        53.26        24.56        52.96        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
        5.85         2.50        13.61         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A1ET TCGA-BH-A1EU 
       44.81         4.90        20.12        72.56        82.85        42.28 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG 
       49.58        25.81        89.16       120.62        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A28O 
       36.92        63.35        55.00       144.59        72.07        10.65 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.12       109.28        20.88         5.26        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A26V 
        9.44        11.77        12.66        12.33        11.28        20.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HR 
       12.36        12.95         0.03        33.99        13.02        13.41 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JN 
       20.58        13.48        21.14        55.50        14.01        20.38 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       12.20        14.70        16.73        25.74        18.15        12.39 
TCGA-D8-A1XM TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.69        15.16        17.42        14.43        48.03        16.41 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
        1.61        13.08        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q 
       12.66        27.52        40.41        28.87        47.15        38.24 
TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D 
       43.33        69.34        21.04        23.87        22.82        17.29 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B1 
       55.63        53.92         9.04        20.58        19.56        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IF TCGA-E2-A1IJ 
       33.01        32.35        28.50        16.47        37.41        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
       59.18         3.88        11.08        54.18        19.66        75.81 
TCGA-E2-A1LE TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       28.90        43.56        30.61        34.82        32.88        36.82 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD 
       35.77        25.84        28.27         6.12        45.01         1.12 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 
       47.64        32.05        37.74        39.09        40.50        20.12 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
        1.94        24.56         9.47        32.91        30.44        23.90 
TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1OX 
       26.70        39.72         8.48        18.21        13.25        29.95 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PE TCGA-EW-A1PG 
       39.78        52.96        18.48        30.08        10.52        34.55 
TCGA-EW-A2FR TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6SC TCGA-GM-A2DA TCGA-GM-A2DB 
       55.00        34.03        23.51        31.30       216.76        79.10 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62        85.35        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        62.47        11.84        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO 
       10.62        24.95        29.23        25.05        17.06        14.47 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        7.46        14.50        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       58.62        40.08        34.92        28.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY 
       65.62        42.77        14.07        19.73        40.11         0.26 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-W8-A86G 
       13.84        18.87        17.39        17.26        66.84        11.41 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       15.35        16.04       108.07 

$subtype3
TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A3XU 
       43.43        20.88        77.19        98.99        56.81        29.98 
TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07Z 
       21.14        33.11        14.70        26.01        18.97        45.07 
TCGA-A8-A084 TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A0A1 
       15.06        28.96        17.95         9.99        12.00        12.00 
TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A5XS TCGA-AC-A62Y 
       19.04        17.03         6.48        14.83        19.33        17.42 
TCGA-AC-A6NO TCGA-AN-A0FK TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03N TCGA-AO-A0J7 
        1.68         7.00        12.33         0.30        66.77        20.32 
TCGA-AO-A0J9 TCGA-AO-A12A TCGA-AR-A0TR TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A5QM 
       53.03        90.58         5.26        61.28        50.89        73.35 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0RH TCGA-B6-A0RP TCGA-B6-A0WW TCGA-B6-A40B 
      129.57       112.37       212.25       102.77        18.35       103.63 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0DP 
       70.22        37.22        21.70        49.94        44.02        15.65 
TCGA-BH-A0E9 TCGA-BH-A0GZ TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18K 
       46.19        10.78        36.85        12.89        32.91        90.84 
TCGA-BH-A18P TCGA-BH-A1EV TCGA-BH-A202 TCGA-BH-A28Q TCGA-BH-A6R8 TCGA-BH-A8FY 
       30.28        12.00        26.14         6.44         9.63         9.70 
TCGA-C8-A274 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
        9.53        14.17        16.50        14.73        55.30        15.85 
TCGA-D8-A27V TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 
       12.53        25.22        34.42        37.51        28.44        23.24 
TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A2P6 
       19.43        18.21        37.25        33.73        73.64        34.55 
TCGA-E9-A1NH TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A249 TCGA-E9-A3HO 
       18.94         2.56         3.02        40.24         7.13        38.07 
TCGA-E9-A6HE TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A3NW TCGA-LD-A66U TCGA-LL-A6FP 
       27.85         6.15        10.16       110.50        21.24        22.26 
TCGA-LQ-A4E4 TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE 
       27.91        41.92        26.04         8.91        64.21        86.96 
TCGA-S3-AA0Z TCGA-WT-AB44 
       20.68        29.03 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       31.79        28.01        19.20        18.02        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ 
       24.79       107.93        67.33        34.55        33.76        79.76 
TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ 
       63.29        50.43        17.52         8.38        18.21        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        91.07        47.31        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA 
       50.83         7.30        21.90        35.31        37.45        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE 
       31.73        20.19        23.74        21.73        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.29         9.37        10.42         8.75 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B 
       31.00        17.03         9.99         8.98        24.99        38.01 
TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09D TCGA-A8-A09N 
        9.99         0.99        43.00        30.97        50.04         1.02 
TCGA-A8-A09Q TCGA-AC-A23C TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A5XU 
       25.02         0.95        73.05        33.04        16.57        14.96 
TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
       13.71         1.12         1.78         1.71         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        7.59         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J6 
        0.33         0.33        61.35        29.13        52.18        37.48 
TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F 
       50.70        55.33       115.27       108.03        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP 
       41.62        70.39        26.93       130.09         2.56       140.55 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
      109.02        75.22        98.93        55.86        65.36       133.22 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H 
      107.21       125.16       108.36        17.23        33.73       160.90 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR 
      104.28        97.84        77.69        99.62        93.83        57.27 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO 
       77.62       143.38        65.72       233.62        18.77       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      140.88       255.68       100.70       282.90        21.47       245.10 
TCGA-B6-A1KF TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AW 
      101.52         7.07        70.16        18.84        59.84        20.45 
TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       39.55        81.63        51.68        43.53        61.51        74.89 
TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 
       75.48        76.60        77.95        41.75         4.41         9.63 
TCGA-BH-A0GY TCGA-BH-A0H9 TCGA-BH-A0WA TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V 
       30.35        41.00        23.05        55.63         7.36        51.16 
TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       17.69        97.48        72.07        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A130 TCGA-C8-A131 
       18.64        11.93        11.77        12.66         3.16        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W 
       12.59        12.92        10.92         0.16        12.33        12.53 
TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        9.50        14.43        20.88        13.97        14.17        19.20 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        53.00        20.09        20.12        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       21.01        18.58        21.80        14.50        19.92        16.41 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M 
       12.99        43.04        15.32        16.04        13.05        13.48 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 
       38.60        31.96        18.51        63.62        14.79        25.05 
TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH 
       11.05        76.57        33.70        60.99        60.36       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 
      102.61        43.04        26.99        34.92        38.76        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22B 
       36.20        39.55        41.62        46.59        34.45        38.37 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1J1 
       41.72        40.73         0.69        30.18         0.79        18.90 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PF 
       25.94        22.82        29.82         7.86        19.99        14.43 
TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SD 
       19.96        25.91        17.49        15.22        24.99        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A7W5 
        7.40       109.87        70.85        69.30         2.60         7.10 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 
       32.75        14.70        14.79        16.08        15.68        19.59 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ 
       58.52        36.36        20.38        23.47        28.21         9.93 
TCGA-S3-AA10 TCGA-UU-A93S 
       19.27         3.81 

$subtype5
TCGA-A2-A0CU TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25D TCGA-A8-A091 TCGA-AC-A6IW 
        5.19        23.47        20.25        18.15        33.01        13.58 
TCGA-AO-A03R TCGA-AO-A1KP TCGA-B6-A0IA TCGA-B6-A1KC TCGA-B6-A2IU TCGA-BH-A0AY 
       68.75        82.62       275.87        43.59       170.17        25.55 
TCGA-BH-A0BT TCGA-BH-A0DS TCGA-BH-A0H0 TCGA-BH-A0HB TCGA-BH-A1EO TCGA-BH-A1FC 
       45.57         2.56        15.16        26.50        91.99       114.15 
TCGA-BH-A1FD TCGA-BH-A204 TCGA-C8-A12X TCGA-D8-A1X6 TCGA-D8-A1XD TCGA-D8-A1Y1 
       33.17        83.31        12.66        17.79        17.16         9.93 
TCGA-D8-A1Y2 TCGA-E2-A10C TCGA-E2-A15F TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1IN 
       14.24        40.11        21.63        56.94        53.62        22.19 
TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1RB TCGA-E9-A54Y 
       50.07         8.75        34.29        22.29        32.09        23.84 
TCGA-EW-A1P0 TCGA-GM-A2DC TCGA-JL-A3YX TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-WT-AB41 
       41.13        83.34        11.57        19.53        17.49        52.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.16     0.03     0.30     0.16     2.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
  162.05   281.29   212.25   282.90   275.87 
subtype1 subtype2 subtype3 subtype4 subtype5 
  24.790   32.550   24.230   25.925   26.025 
[1] "0.2 - 162.1 (24.8)" "0.0 - 281.3 (32.5)" "0.3 - 212.2 (24.2)"
[4] "0.2 - 282.9 (25.9)" "2.6 - 275.9 (26.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      13       18        2        1        88        66         1
  subtype2      48       44        4        3       112        87         1
  subtype3       6        4        0        1        32        29         0
  subtype4      19       16        0        1       104        59         0
  subtype5       3        3        0        0        17        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         48         13         14        8         0       3
  subtype2         58          6         29        7         0       7
  subtype3          9          4          8        2         0       2
  subtype4         33          6         11        3         1       1
  subtype5          6          0          3        0         0       0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          13       48        6       19        3
  STAGE IA         18       44        4       16        3
  STAGE IB          2        4        0        0        0
  STAGE II          1        3        1        1        0
  STAGE IIA        88      112       32      104       17
  STAGE IIB        66       87       29       59       11
  STAGE III         1        1        0        0        0
  STAGE IIIA       48       58        9       33        6
  STAGE IIIB       13        6        4        6        0
  STAGE IIIC       14       29        8       11        3
  STAGE IV          8        7        2        3        0
  STAGE TIS         0        0        0        1        0
  STAGE X           3        7        2        1        0
[1] 13  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  57 177  26  14
  subtype2 144 185  68   9
  subtype3  12  64  15   7
  subtype4  50 173  23   9
  subtype5  13  25   4   1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       57      144       12       50       13
  T2      177      185       64      173       25
  T3       26       68       15       23        4
  T4       14        9        7        9        1
[1] 4 5
[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
  subtype1 104 102  42  18
  subtype2 199 133  35  32
  subtype3  44  35   6  11
  subtype4 143  70  31  13
  subtype5  17  18   5   3
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0      104      199       44      143       17
  N1      102      133       35       70       18
  N2       42       35        6       31        5
  N3       18       32       11       13        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus         0   1
  subtype1 234   9
  subtype2 320   7
  subtype3  80   2
  subtype4 221   4
  subtype5  34   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  234    9
  subtype2  320    7
  subtype3   80    2
  subtype4  221    4
  subtype5   34    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      234      320       80      221       34
  1        9        7        2        4        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1 264  11
  subtype2 407   0
  subtype3  97   1
  subtype4 257   0
  subtype5  43   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  264   11
  subtype2  407    0
  subtype3   97    1
  subtype4  257    0
  subtype5   43    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      264      407       97      257       43
  MALE         11        0        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1 115 130
  subtype2 161 192
  subtype3  32  53
  subtype4 105 124
  subtype5  16  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  115  130
  subtype2  161  192
  subtype3   32   53
  subtype4  105  124
  subtype5   16   19
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO       115      161       32      105       16
  YES      130      192       53      124       19
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           230
  subtype2                          0                           229
  subtype3                          0                            53
  subtype4                          1                           229
  subtype5                          0                            29
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             26                   0
  subtype2                            123                   0
  subtype3                             37                   0
  subtype4                              6                   5
  subtype5                              8                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                6
  subtype2                     6                               14
  subtype3                     0                                5
  subtype4                     3                                4
  subtype5                     0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  4              9
  subtype2                 12             23
  subtype3                  0              3
  subtype4                  0              8
  subtype5                  1              4
D3V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA         230      229       53      229       29
  INFILTRATING LOBULAR CARCINOMA         26      123       37        6        8
  MEDULLARY CARCINOMA                     0        0        0        5        1
  METAPLASTIC CARCINOMA                   0        6        0        3        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        6       14        5        4        0
  MUCINOUS CARCINOMA                      4       12        0        0        1
  OTHER  SPECIFY                          9       23        3        8        4
[1] 8 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    22                        41
  subtype2                                1    18                        54
  subtype3                                0     3                         9
  subtype4                                0    15                        70
  subtype5                                0     2                         7
          vv
clus       WHITE
  subtype1   172
  subtype2   312
  subtype3    74
  subtype4   155
  subtype5    32
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                  22       18        3       15        2
  BLACK OR AFRICAN AMERICAN              41       54        9       70        7
  WHITE                                 172      312       74      155       32
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
          cls
clus         0   1
  subtype1   9 214
  subtype2  17 339
  subtype3   3  73
  subtype4   9 213
  subtype5   1  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  214
  subtype2   17  339
  subtype3    3   73
  subtype4    9  213
  subtype5    1   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            9       17        3        9        1
  NOT HISPANIC OR LATINO      214      339       73      213       36
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 129  18
  subtype2  81  20
  subtype3 194  21
  subtype4 107  16
  subtype5 111  25
  subtype6  57   2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     147      101      215      123      136       59 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       20       21       16       25        2 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04R 
      129.14       131.67        42.81        13.68        18.21       121.94 
TCGA-A2-A0CT TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV 
       75.25        20.75        21.90        21.67        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A4S3 
       17.36        60.72        19.56        42.44       105.34        21.90 
TCGA-A7-A0D9 TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A8-A075 
       37.45        20.61        22.32        17.92        14.73        17.03 
TCGA-A8-A08O TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3W5 TCGA-AC-A5EH 
       31.00         5.72        99.35        26.04        16.57        16.80 
TCGA-AC-A62V TCGA-AC-A8OP TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0JA 
       11.44        20.19         0.33        80.28        61.35        21.53 
TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ 
       72.00        26.24        50.24        65.56        82.62        61.87 
TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A24L 
        0.53        98.33        98.93        83.87       134.14        94.22 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-B6-A0IK TCGA-B6-A0RG TCGA-B6-A0RO TCGA-B6-A0WV 
       98.66        89.00        18.77        68.45       162.05        79.63 
TCGA-B6-A0WY TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU 
      113.79        68.94        43.59       139.17        68.12        62.93 
TCGA-BH-A0AW TCGA-BH-A0B8 TCGA-BH-A0BZ TCGA-BH-A0E2 TCGA-BH-A0GY TCGA-BH-A0H7 
       20.45        51.58        49.05        14.30        30.35        23.08 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HX TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1F2 
       52.96        26.50        27.25        91.99       113.82        31.53 
TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A204 TCGA-BH-A6R8 TCGA-C8-A1HG TCGA-C8-A1HK 
       24.62        45.63        83.31         9.63        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42        12.33        12.95        12.33        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A1JA 
        9.67         0.03        24.56        12.49        19.46        16.50 
TCGA-D8-A1JC TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XY 
       15.78        18.58        23.90        17.16        15.22        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A106 
       15.32        15.52        10.09        12.26        43.00        83.54 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A15K TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       46.59        40.11         9.04        77.65        70.36        33.73 
TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1R7 
        8.28        22.29        36.20         9.86        11.15        48.23 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A295 
       46.65         6.58        21.27        42.25        38.37        12.33 
TCGA-E9-A2JS TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       29.72        25.81        18.90        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FS TCGA-EW-A2FV 
       40.41        18.90         6.15        14.43        52.73        25.91 
TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2DC TCGA-GM-A2DK TCGA-LL-A7T0 
       15.22        31.30         7.40        83.34        86.96        12.36 
TCGA-LL-A9Q3 TCGA-OL-A5RZ TCGA-OL-A66J TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZH 
       17.49        22.32        65.62        17.36        18.81        21.07 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-UL-AAZ6 
       13.84        18.87        17.03 

$subtype2
TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0SV TCGA-A2-A0SW 
       40.14         9.96        48.10        39.32        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3XV 
       44.28        20.52        18.90        18.15        36.23        32.75 
TCGA-A7-A26H TCGA-A7-A4SC TCGA-AC-A23C TCGA-AC-A3EH TCGA-AC-A4ZE TCGA-AC-A5XU 
       23.80        14.66         0.95         6.48        29.26        14.96 
TCGA-AC-A7VB TCGA-AN-A0XN TCGA-AN-A0XV TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12E 
        8.22         0.33         5.33        76.77        71.80        57.30 
TCGA-AO-A12G TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TV 
       41.62        17.79        24.79       130.09         5.65        75.22 
TCGA-AR-A0TZ TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24N 
      107.24        93.90        41.82        61.28       160.90        99.78 
TCGA-AR-A24R TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QN 
      112.77        71.05        54.21        66.15        73.35        33.30 
TCGA-B6-A0RL TCGA-B6-A0WW TCGA-B6-A40B TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0DS 
       81.17        18.35       103.63        45.83        13.91         2.56 
TCGA-BH-A0HK TCGA-BH-A0HY TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1FD 
        5.85        50.79        67.50        12.00        17.69        33.17 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A42T TCGA-BH-AB28 TCGA-C8-A26V TCGA-C8-A274 
       26.14        38.60        10.52         9.44        20.25         9.53 
TCGA-C8-A3M8 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JN 
       12.95        14.17        17.49        12.03        20.09        20.38 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N TCGA-E2-A1L7 
       21.80        12.99        14.14        13.45         4.80        60.36 
TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1NA 
       28.90        26.99        34.55        34.29        17.69        36.56 
TCGA-E9-A1NF TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A247 TCGA-EW-A1IW TCGA-EW-A3E8 
       35.24         3.02        40.24        38.99        12.20        34.03 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-GM-A2DL TCGA-GM-A3NY TCGA-LL-A5YL 
       10.16        23.51        16.77       115.69        38.20        17.06 
TCGA-LL-A5YM TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-OL-A5D8 TCGA-OL-A66K TCGA-OL-A66L 
       15.32        14.50        27.91        31.99        41.92        42.77 
TCGA-OL-A66N TCGA-PE-A5DC TCGA-PE-A5DD TCGA-S3-A6ZG TCGA-S3-AA17 
       26.04        47.01        64.21        18.48        13.94 

$subtype3
TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       11.44        48.56        43.43        14.27        47.24        20.88 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0EU TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD 
      136.73       114.81        34.29        17.46        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YL TCGA-A2-A1G0 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A3KD 
       50.47        48.46        20.25       107.70        17.19        39.65 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       23.21        21.14        25.15        23.61        29.56        31.36 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SB TCGA-A7-A6VX TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2FG 
       13.74        10.42        38.04        22.95         1.48        60.92 
TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       19.33        16.31        22.19        24.13        25.05        14.99 
TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A0XL 
       24.79        17.42         1.68         1.32         2.30         5.36 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AO-A03N TCGA-AO-A0JF 
       12.33         0.30         0.33         0.33        66.77        65.10 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       62.04        99.25       108.72        98.27        15.62        32.52 
TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AS 
       32.91         5.26       103.86        97.68        98.33        37.81 
TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24P TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A2LE 
       50.89       120.33         2.76       105.30        98.76       166.42 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
       63.62        38.17       234.28        78.02       263.28       102.77 
TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A2IU 
      188.68       206.86        28.27        58.88        73.51       170.17 
TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ 
       71.15        63.09        70.22        37.22        32.02        21.70 
TCGA-BH-A0BM TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DH TCGA-BH-A0DP TCGA-BH-A0DQ 
       61.68        53.95        45.57        38.01        15.65         3.22 
TCGA-BH-A0E1 TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HN 
       15.68        15.16        24.56        23.90        20.38        16.96 
TCGA-BH-A0HP TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 
       13.61        23.93        24.95        82.85        49.58        89.16 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A28Q TCGA-BH-A5J0 
      122.89        63.35        55.00       144.59         6.44        23.51 
TCGA-BH-A8FY TCGA-C8-A1HE TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS 
        9.70        12.33        18.15        18.90        18.97        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA 
       13.32        14.70        17.79        16.73        25.74        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       18.15        12.39        14.73        55.30        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A1Y1 TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A27T 
       15.16         9.93        17.42        48.03         1.61        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 
       12.53        33.37        18.51        12.66        25.22        34.42 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A1B4 
       37.51        28.44        28.87        55.63        53.92        33.01 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       16.47        37.25        37.41         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A570 TCGA-E2-A572 
       11.08        54.18        73.64        19.66        30.61        39.72 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R3 
       34.82        32.88        36.82        18.94        28.27         2.56 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22H 
        1.12        47.64        34.45        32.05        37.74        40.50 
TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UP 
        7.13        38.07        32.91        23.90        23.84        26.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1P0 
       27.85        39.72        13.25        16.57        15.68        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PE TCGA-EW-A2FW TCGA-GM-A2D9 
       52.96        23.11        18.48        10.52        22.09        59.57 
TCGA-GM-A3NW TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
      110.50        13.55        18.12        62.47        11.57        21.24 
TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-MS-A51U 
       13.28        29.23        25.05        22.26         2.63        22.39 
TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A66H TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LX 
       58.62        34.92        26.70        19.73        40.11         0.16 
TCGA-S3-AA14 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB44 TCGA-Z7-A8R6 
       17.39        66.84        11.41        29.03       107.05 

$subtype4
TCGA-5L-AAT1 TCGA-A2-A0CR TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ST TCGA-A2-A0T1 
       48.36       107.93        89.36       118.45        99.19        17.13 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A25F TCGA-A2-A3XZ TCGA-A7-A4SA TCGA-AC-A23G 
       49.48        19.33        10.59        50.37        14.93        73.91 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3W6 
       40.57        86.66        90.71        74.14        32.45        19.79 
TCGA-AC-A5XS TCGA-AC-A6IV TCGA-AC-A8OQ TCGA-AN-A0XW TCGA-AO-A03U TCGA-AO-A0JC 
       19.33        18.67         1.12         5.59        58.95        50.86 
TCGA-AO-A128 TCGA-AQ-A7U7 TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AO 
      106.78        19.20       109.02        64.83       101.00        86.07 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A252 
       86.53        86.43       118.59        97.84        77.69        93.30 
TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0RT TCGA-B6-A3ZX TCGA-B6-A401 TCGA-BH-A0B6 
       20.25        10.59        89.46        37.87        85.35        81.63 
TCGA-BH-A0BF TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DV TCGA-BH-A0RX TCGA-BH-A0W5 
       43.53        41.75        89.06        67.86         5.59        42.35 
TCGA-BH-A1EU TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FU TCGA-BH-A209 
       42.28        25.81       120.62        74.73        72.07       130.16 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A26W 
       20.12       109.28         5.26        18.87        21.76        12.53 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A1Y2 
       12.36         9.50        33.99        13.02        13.41        14.24 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A73U TCGA-E2-A108 TCGA-E2-A1B1 
       14.43        16.41        13.48        16.18        27.52        87.22 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1LA 
       32.35        28.50        33.70        28.44        59.18        24.59 
TCGA-E2-A3DX TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A22D 
       43.56        35.77        25.84        24.82         6.12        41.03 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK 
       20.12         1.94         9.47        30.18        30.44        26.70 
TCGA-EW-A1IZ TCGA-EW-A1OV TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PG TCGA-EW-A3U0 
       18.21        25.94        39.78        30.08        34.55        17.49 
TCGA-EW-A6SB TCGA-GM-A2DA TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       24.99       216.76        75.02        70.85        72.10        85.15 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A4E0 TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 
      101.62        85.35        72.03         7.10        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-OK-A5Q2 TCGA-OL-A5RU 
       32.75        14.70        14.47        19.53         2.10        40.08 
TCGA-OL-A5RY TCGA-OL-A66I TCGA-OL-A66P TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-AA15 
       24.72        23.47        14.07        86.96         9.93        17.26 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       52.96        15.35        16.04 

$subtype5
TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A0SX TCGA-A2-A0T0 
        8.52        31.79        28.01        19.20        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS 
        8.38        18.21        18.61        31.73        19.20        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       91.07        29.98        47.31        35.93        50.83        24.39 
TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       26.96        31.73        20.19        24.26        23.74        21.73 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.50        21.17        12.10        10.29         9.37         8.75 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5EI TCGA-AC-A62X TCGA-AC-A6IW 
       73.05        33.04        14.66        14.53        13.71        13.58 
TCGA-AC-A7VC TCGA-AN-A0XU TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 
        0.03         0.33        50.70        55.33       115.27       108.03 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TU TCGA-AR-A0U0 
       14.73        70.39         2.56       140.55        23.31        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
      107.21       108.36        96.00        99.32        17.23        33.73 
TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0RE 
      104.28        99.62        93.83        57.27        77.62       255.68 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A400 
      100.70       282.90        21.47       245.10       101.52         7.07 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0E0 TCGA-BH-A0H9 
       70.16        18.84        39.55        51.68         4.41        41.00 
TCGA-BH-A0WA TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5IZ 
       23.05        97.48       114.15        72.07        57.83        18.64 
TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
        0.16        14.43        53.00        20.12        20.09        19.40 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H 
       14.50        16.41        16.64        43.04        16.04        13.05 
TCGA-E2-A14N TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       47.15        76.57        53.62        50.07       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 
        8.75        43.04        52.73        34.92        38.76        34.16 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22E TCGA-E9-A22G 
       39.55        41.62        32.09        46.59        41.72        40.73 
TCGA-E9-A244 TCGA-E9-A24A TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
        0.69        24.56         0.79        22.82        29.82         7.86 
TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A3XL 
       19.99        19.96        33.21       109.87        79.10        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        2.60        11.84        14.79        16.08        15.68         7.46 
TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A6VO 
       19.59        36.30        58.52        36.36        20.38        28.21 
TCGA-OL-A97C TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UU-A93S 
        8.91        20.68        19.27         3.81 

$subtype6
TCGA-A1-A0SM TCGA-A2-A0SU TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A3XW 
        7.96        54.64        22.45        16.47        52.47        56.28 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A7-A3IY TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A0A6 
        7.30        21.30        11.34        10.72        11.05        21.04 
TCGA-AC-A2FK TCGA-AC-A3OD TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A6IX TCGA-AR-A1AU 
       87.12        14.83        15.48        23.24        12.26        94.29 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A2LJ TCGA-AR-A2LO TCGA-AR-A2LQ 
      105.27        32.58        85.64        86.53        39.39        40.54 
TCGA-AR-A5QP TCGA-B6-A0RV TCGA-BH-A0B2 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0GZ 
       38.96       157.41        40.83        23.44        29.98        10.78 
TCGA-BH-A0H3 TCGA-BH-A1EW TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42V 
       37.78        55.69        36.92        28.14        10.65        20.88 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1XL 
       10.92        11.28        55.50        14.01        21.01        19.92 
TCGA-D8-A1XM TCGA-D8-A4Z1 TCGA-E2-A14U TCGA-E2-A1LB TCGA-E9-A1R2 TCGA-E9-A1RA 
       17.69        21.67        43.33        75.81        34.95        45.01 
TCGA-E9-A22A TCGA-EW-A1IY TCGA-EW-A1PD TCGA-EW-A2FR TCGA-GM-A2DM TCGA-GM-A3XG 
       39.09         8.48        13.94        55.00       106.06        43.73 
TCGA-GM-A3XN TCGA-LD-A74U TCGA-OL-A5RX TCGA-PL-A8LY TCGA-Z7-A8R5 
       66.38        13.22        28.87         0.26       108.07 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.33     0.16     1.12     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  162.05   160.90   263.28   216.76   282.90   157.41 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   23.90    27.12    25.22    32.45    29.90    28.87 
[1] "0.0 - 162.1 (23.9)" "0.3 - 160.9 (27.1)" "0.2 - 263.3 (25.2)"
[4] "1.1 - 216.8 (32.5)" "0.0 - 282.9 (29.9)" "0.3 - 157.4 (28.9)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       7        6        1        0        44        39         0
  subtype2       7        9        0        2        27        22         1
  subtype3      17       23        2        2        58        56         0
  subtype4      18        9        0        2        43        21         1
  subtype5       6        8        1        0        61        37         0
  subtype6       6        7        1        0        11        12         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         28          9          9        2       1
  subtype2         20          1          9        2       1
  subtype3         37          5         13        1       2
  subtype4         18          2          7        2       0
  subtype5         14          2          3        3       1
  subtype6          9          0         12        1       0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           7        7       17       18        6        6
  STAGE IA          6        9       23        9        8        7
  STAGE IB          1        0        2        0        1        1
  STAGE II          0        2        2        2        0        0
  STAGE IIA        44       27       58       43       61       11
  STAGE IIB        39       22       56       21       37       12
  STAGE III         0        1        0        1        0        0
  STAGE IIIA       28       20       37       18       14        9
  STAGE IIIB        9        1        5        2        2        0
  STAGE IIIC        9        9       13        7        3       12
  STAGE IV          2        2        1        2        3        1
  STAGE X           1        1        2        0        1        0
[1] 12  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  26  91  19  10
  subtype2  22  58  19   2
  subtype3  63 115  32   5
  subtype4  46  61  14   2
  subtype5  24  92  15   5
  subtype6  20  29  10   0
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       26       22       63       46       24       20
  T2       91       58      115       61       92       29
  T3       19       19       32       14       15       10
  T4       10        2        5        2        5        0
[1] 4 6
[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
  subtype1 52 61 21 10
  subtype2 47 25 17  9
  subtype3 89 85 24 13
  subtype4 59 41 15  8
  subtype5 81 38 12  5
  subtype6 22 19  6 12
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       52       47       89       59       81       22
  N1       61       25       85       41       38       19
  N2       21       17       24       15       12        6
  N3       10        9       13        8        5       12
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1 121   2
  subtype2  70   3
  subtype3 168   1
  subtype4  92   2
  subtype5 111   4
  subtype6  47   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  121    2
  subtype2   70    3
  subtype3  168    1
  subtype4   92    2
  subtype5  111    4
  subtype6   47    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      121       70      168       92      111       47
  1        2        3        1        2        4        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1 145   2
  subtype2  98   3
  subtype3 214   2
  subtype4 123   0
  subtype5 137   0
  subtype6  57   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  145    2
  subtype2   98    3
  subtype3  214    2
  subtype4  123    0
  subtype5  137    0
  subtype6   57    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      145       98      214      123      137       57
  MALE          2        3        2        0        0        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus        0  1
  subtype1 61 74
  subtype2 38 53
  subtype3 90 98
  subtype4 49 64
  subtype5 54 69
  subtype6 17 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   74
  subtype2   38   53
  subtype3   90   98
  subtype4   49   64
  subtype5   54   69
  subtype6   17   33
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        61       38       90       49       54       17
  YES       74       53       98       64       69       33
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           123
  subtype2                          0                            59
  subtype3                          0                           109
  subtype4                          0                            76
  subtype5                          1                           110
  subtype6                          0                            36
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             11                   0
  subtype2                             35                   0
  subtype3                             70                   0
  subtype4                             38                   2
  subtype5                              4                   4
  subtype6                             20                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                5
  subtype2                     0                                4
  subtype3                     0                               11
  subtype4                     2                                3
  subtype5                     7                                1
  subtype6                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  4              4
  subtype2                  0              3
  subtype3                 10             16
  subtype4                  0              2
  subtype5                  0              9
  subtype6                  1              1
D4V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         123       59      109       76      110
  INFILTRATING LOBULAR CARCINOMA         11       35       70       38        4
  MEDULLARY CARCINOMA                     0        0        0        2        4
  METAPLASTIC CARCINOMA                   0        0        0        2        7
  MIXED HISTOLOGY (PLEASE SPECIFY)        5        4       11        3        1
  MUCINOUS CARCINOMA                      4        0       10        0        0
  OTHER  SPECIFY                          4        3       16        2        9
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          36
  INFILTRATING LOBULAR CARCINOMA         20
  MEDULLARY CARCINOMA                     0
  METAPLASTIC CARCINOMA                   0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      1
  OTHER  SPECIFY                          1
[1] 8 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    14                        34
  subtype2                                0     4                        20
  subtype3                                0     5                        20
  subtype4                                1     8                        25
  subtype5                                0     4                        52
  subtype6                                0     3                         9
          vv
clus       WHITE
  subtype1    97
  subtype2    74
  subtype3   188
  subtype4    86
  subtype5    78
  subtype6    46
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                  14        4        5        8        4
  BLACK OR AFRICAN AMERICAN              34       20       20       25       52
  WHITE                                  97       74      188       86       78
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   3
  BLACK OR AFRICAN AMERICAN               9
  WHITE                                  46
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus         0   1
  subtype1   8 127
  subtype2   7  88
  subtype3   8 185
  subtype4   5 107
  subtype5   7 117
  subtype6   3  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  127
  subtype2    7   88
  subtype3    8  185
  subtype4    5  107
  subtype5    7  117
  subtype6    3   52
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            8        7        8        5        7        3
  NOT HISPANIC OR LATINO      127       88      185      107      117       52
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 123  27
  subtype2 106  16
  subtype3 110  16
subtype1 subtype2 subtype3 
     150      122      126 
subtype1 subtype2 subtype3 
      27       16       16 
$subtype1
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       47.24        31.79        28.01        18.02        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CX 
      101.98        36.13        99.12        24.79       107.93        56.81 
TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY 
       55.00        67.33        34.55        33.76        79.76        63.29 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        44.88        50.43        17.52        17.13         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE 
       18.21        21.90        21.67        18.61        31.73        35.31 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A06R TCGA-A8-A06U 
       30.61        35.67        31.73        20.19        17.98        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07R 
       31.00        26.01        17.03        14.01         9.99         8.98 
TCGA-A8-A07W TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A09A 
        9.99        37.05         9.99        31.00        43.00         9.99 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04D 
       45.07        33.07         8.98        14.01         0.99         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0G0 TCGA-AN-A0XU 
        7.96         7.59         0.33         0.33         0.53         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03U TCGA-AO-A0J2 
        5.59        80.28        66.77        81.63        58.95        32.78 
TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 
       37.48        50.70        72.00        76.77        55.33       115.27 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
      108.03        64.04        48.36       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 
      109.02        23.31        75.22        98.93        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AO TCGA-AR-A1AQ 
      133.22       134.14       125.16       108.36        86.07        99.32 
TCGA-AR-A1AT TCGA-AR-A1AY TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       41.82        33.73        32.58        12.13       233.62       140.88 
TCGA-B6-A0RU TCGA-B6-A0X1 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BF 
      282.90       245.10        40.83        39.55        51.68        43.53 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0E0 
       77.95        49.05        41.75        89.06        78.28         4.41 
TCGA-BH-A0E2 TCGA-BH-A0EE TCGA-BH-A18G TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       14.30        31.00         4.90        30.28        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18V TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        7.36        51.16        11.93        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A13Z 
        1.87        12.59         4.11         4.08        56.81        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-E2-A14P TCGA-E2-A14Y TCGA-E2-A14Z 
       13.97        14.17        19.20        40.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1AZ 
       63.62        69.96        14.79        25.05        20.71        76.57 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER 
       13.68       143.15        78.41        92.48        53.13        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       72.00        34.29        31.82        61.94        24.72        99.19 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF 
       49.84        20.52        18.90        20.75        32.55        50.47 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A7-A0D9 TCGA-A8-A06P TCGA-A8-A076 
       19.33        48.46        23.77        37.45        13.02        53.98 
TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A084 TCGA-A8-A08O 
        9.01        19.99        18.97        10.98        15.06        31.00 
TCGA-A8-A095 TCGA-A8-A09B TCGA-A8-A09K TCGA-A8-A0A4 TCGA-AN-A041 TCGA-AN-A0FS 
       41.98        12.00        29.98        13.02         0.23         6.90 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A03M TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0J9 
        0.33         0.33        61.35        26.04        22.36        53.03 
TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12E 
       65.10        50.24        62.04        71.80       106.78        57.30 
TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ 
      130.09        64.83       107.24        83.87       107.21       101.00 
TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-B6-A0I2 
       97.68        93.90        94.29        86.53        86.43       143.38 
TCGA-B6-A0I8 TCGA-B6-A0IK TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RN TCGA-B6-A0RO 
       24.62        18.77        68.45       212.25       263.28       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WX TCGA-BH-A0AU TCGA-BH-A0AV 
      140.48        89.46       157.41        21.47        62.93        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       25.55        63.09        81.44        39.16        70.22        84.13 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       37.22        32.02        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP 
       76.60        45.57        44.02        23.44        29.98        15.65 
TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
        2.56        67.86        15.68         9.63        46.19        32.58 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HN TCGA-BH-A0HP 
       24.43        30.35        24.56        23.08        16.96        13.61 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18U 
       50.79         5.59        20.12        26.66        72.56        51.39 
TCGA-C8-A12N TCGA-C8-A131 TCGA-C8-A135 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14T 
       11.77        13.51        12.92        27.52        40.11        75.98 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A1B0 TCGA-E2-A1B1 
       34.26        31.96        22.82        21.63        53.62        87.22 
TCGA-E2-A1B5 TCGA-E2-A1B6 
       32.35        28.50 

$subtype3
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       63.12        88.60        77.19        75.25         5.19        98.99 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD 
       61.58        25.22        80.28        54.64        17.46        25.28 
TCGA-A2-A0YI TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A0DC 
       49.48        38.30        34.29        35.47        33.11        29.79 
TCGA-A7-A13F TCGA-A8-A06Z TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 
       25.15         1.02         7.99        45.07        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A099 
        0.99        19.96       112.08        40.01        33.01         9.99 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09W TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ 
        1.02        49.05         0.99         0.62         2.96         9.96 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ 
        6.44         5.65         7.00         7.04         0.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A0J3 
       12.33         0.30         0.33         0.33        95.70        21.40 
TCGA-AO-A0J7 TCGA-AO-A0JC TCGA-AO-A0JG TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B 
       20.32        50.86        26.24       108.72        90.58        98.27 
TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AS 
       65.56        41.62        40.57         5.26       103.86        37.81 
TCGA-AR-A1AV TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RL TCGA-B6-A0RM 
       61.28       129.57       146.50       165.76        81.17        78.02 
TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-BH-A0B1 TCGA-BH-A0BJ TCGA-BH-A0BS TCGA-BH-A0BV 
      102.77       129.70        37.74        21.70        53.95        49.94 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DT TCGA-BH-A0E7 
       90.97        45.83        38.01        13.91        38.47        44.81 
TCGA-BH-A0EB TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL 
       24.49        53.26        41.00        52.96         5.85         2.37 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F 
       12.89        51.32        27.25        24.95        42.35        32.91 
TCGA-BH-A18N TCGA-BH-A18S TCGA-C8-A12M TCGA-C8-A12X TCGA-D8-A140 TCGA-D8-A145 
       37.74        66.05        11.77        12.66        13.25        13.48 
TCGA-D8-A146 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       21.14        34.42        46.59        40.41        37.51        28.44 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 
       44.68        38.24        33.17        32.02        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H 
       21.04        23.87        23.34        17.29        18.21        12.92 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD 
       56.94        14.07        51.39        33.01        16.47        37.25 

subtype1 subtype2 subtype3 
    0.16     0.23     0.30 
subtype1 subtype2 subtype3 
  282.90   263.28   165.76 
subtype1 subtype2 subtype3 
  32.680   41.045   33.060 
[1] "0.2 - 282.9 (32.7)" "0.2 - 263.3 (41.0)" "0.3 - 165.8 (33.1)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       8        7        0        56        40         23          2
  subtype2      16       11        2        34        22         26          6
  subtype3      12       11        0        45        35         13          5
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1         10        7       1
  subtype2          4        3       2
  subtype3          1        3       3
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8       16       12
  STAGE IA          7       11       11
  STAGE IB          0        2        0
  STAGE IIA        56       34       45
  STAGE IIB        40       22       35
  STAGE IIIA       23       26       13
  STAGE IIIB        2        6        5
  STAGE IIIC       10        4        1
  STAGE IV          7        3        3
  STAGE X           1        2        3
[1] 10  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  22 108  22   4
  subtype2  41  58  18   9
  subtype3  31  81  10   5
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       41       31
  T2      108       58       81
  T3       22       18       10
  T4        4        9        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 71 50 20 12
  subtype2 58 38 21  7
  subtype3 65 45 10  6
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       71       58       65
  N1       50       38       45
  N2       20       21       10
  N3       12        7        6
[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"
D5V6, binary
          cls
clus         0   1
  subtype1 147   8
  subtype2 119   4
  subtype3 121   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  147    8
  subtype2  119    4
  subtype3  121    3
   clus
vv  subtype1 subtype2 subtype3
  0      147      119      121
  1        8        4        3
[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"
D5V7, binary
          cls
clus         0   1
  subtype1 156   0
  subtype2 125   1
  subtype3 124   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  156    0
  subtype2  125    1
  subtype3  124    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      156      125      124
  MALE          0        1        4
[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"
D5V8, binary
          cls
clus        0  1
  subtype1 59 75
  subtype2 43 62
  subtype3 59 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   75
  subtype2   43   62
  subtype3   59   51
     clus
vv    subtype1 subtype2 subtype3
  NO        59       43       59
  YES       75       62       51
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                           143                              4
  subtype2                           101                             21
  subtype3                           110                              6
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   1                                1
  subtype2                   0                                2
  subtype3                   0                                4
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              7
  subtype2                  0              2
  subtype3                  2              6
D5V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING DUCTAL CARCINOMA         143      101      110
  INFILTRATING LOBULAR CARCINOMA          4       21        6
  MEDULLARY CARCINOMA                     1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        2        4
  MUCINOUS CARCINOMA                      0        0        2
  OTHER  SPECIFY                          7        2        6
[1] 6 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    17                        13
  subtype2                                0     4                         8
  subtype3                                0     6                         8
          vv
clus       WHITE
  subtype1   100
  subtype2    98
  subtype3    97
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  17        4        6
  BLACK OR AFRICAN AMERICAN              13        8        8
  WHITE                                 100       98       97
[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"
D5V12, binary
          cls
clus         0   1
  subtype1   2 116
  subtype2   2  89
  subtype3   2  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  116
  subtype2    2   89
  subtype3    2   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        2
  NOT HISPANIC OR LATINO      116       89       93
[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(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 53 10
  subtype2 42  6
  subtype3 76 15
  subtype4 47  7
  subtype5 95 16
  subtype6 26  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      63       48       91       54      111       31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      10        6       15        7       16        5 
$subtype1
TCGA-A1-A0SH TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EO 
       47.24        88.60        77.19        98.99        61.58        80.28 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
       54.64        17.46        25.28        38.30        35.47        30.61 
TCGA-A7-A0DB TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08T 
       33.11         7.99        45.07        13.02         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-AN-A0FF 
       40.01         9.99        12.00         1.02        49.05         5.65 
TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS 
        7.00         0.36         0.33        12.33         0.30         0.33 
TCGA-AO-A12A TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-B6-A0RL TCGA-B6-A0RM 
       90.58         5.26        37.81        61.28        81.17        78.02 
TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-BH-A0B2 TCGA-BH-A0DH TCGA-BH-A0DT TCGA-BH-A0E7 
      102.77       129.70        40.83        38.01        38.47        44.81 
TCGA-BH-A0EB TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18N TCGA-C8-A12Y TCGA-D8-A146 
       24.49        24.95        42.35        37.74        48.53        21.14 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A14Q TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 
       40.41        37.51        38.24        18.51        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15J 
       23.87        17.29        20.71        21.63        18.21        53.92 
TCGA-E2-A15O TCGA-E2-A1B4 TCGA-E2-A1BD 
       50.79        33.01        37.25 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0T4 TCGA-A2-A0T6 
       13.68        34.29        31.82        61.94        20.52        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A8-A07P 
       20.75        49.48        48.46        23.77        34.29        10.98 
TCGA-AN-A049 TCGA-AN-A0XN TCGA-AO-A0J8 TCGA-AO-A0JF TCGA-AO-A12C TCGA-AR-A1AK 
        0.62         0.33        22.36        65.10        65.56       103.86 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-BH-A0AU 
       94.29        86.53       165.76       162.05       140.48        62.93 
TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BO TCGA-BH-A0BP 
       25.55        37.74        32.02        21.70        72.23        75.48 
TCGA-BH-A0BR TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0H6 
       76.60         2.56        46.19        32.58        30.35        24.56 
TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A18F TCGA-BH-A18M TCGA-C8-A12N TCGA-D8-A145 
       16.96        13.61        32.91        72.56        11.77        13.48 
TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A15C TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1BC 
       44.68        75.98        22.82        19.56        87.22        16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL 
       31.79        28.01        18.02        73.84        87.25        99.12 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ST 
       24.79        67.33        34.55        33.76        79.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A075 TCGA-A8-A076 
       35.31        35.67        31.73        20.19        17.03        53.98 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A08L TCGA-A8-A08P TCGA-AN-A04D TCGA-AN-A0AL 
        9.99         8.98         9.99        31.00         1.71         7.46 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 
        0.33         0.33         7.96         7.59         0.33         0.53 
TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 
        0.33        58.95        32.78        37.48        55.33       115.27 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
      106.78       108.03        48.36       140.55        84.10        23.31 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22        83.87       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-B6-A0I6 TCGA-B6-A0IJ 
      101.00        86.07        99.32        33.73        32.58       233.62 
TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      140.88       212.25        89.46       282.90        21.47       245.10 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 
       59.84        39.55        51.68        77.95        78.28         4.41 
TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-C8-A12P TCGA-C8-A12U 
        4.90        55.63         7.36        51.16        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
       12.66        13.51        12.59        20.88        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       19.20        31.96        63.62        14.79        25.05        76.57 
TCGA-E2-A1B6 
       28.50 

$subtype4
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER TCGA-A2-A0ES 
      143.15        78.41        92.48        53.13        74.40        72.00 
TCGA-A2-A0EX TCGA-A2-A0T3 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YK TCGA-A7-A0D9 
       24.72        49.84        32.55        50.47        19.33        37.45 
TCGA-A8-A06P TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A084 TCGA-A8-A08O TCGA-A8-A095 
       13.02        19.99        18.97        15.06        31.00        41.98 
TCGA-AN-A041 TCGA-AO-A0J5 TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AR-A0TZ TCGA-AR-A1AL 
        0.23        26.04        71.80       130.09       107.24        97.68 
TCGA-AR-A1AX TCGA-B6-A0I2 TCGA-B6-A0I8 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RN 
       86.43       143.38        24.62       146.50        18.77       263.28 
TCGA-B6-A0RV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BM 
      157.41        63.09        81.44        70.22        37.22        61.68 
TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DV 
       45.57        44.02        23.44        29.98        15.65        67.86 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0RX 
       15.68         9.63        24.43        23.08        50.79         5.59 
TCGA-BH-A18J TCGA-BH-A18U TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A1B0 TCGA-E2-A1B5 
       20.12        51.39        27.52        40.11        53.62        32.35 

$subtype5
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CY 
       63.12        36.13        75.25         5.19       107.93        55.00 
TCGA-A2-A0D4 TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YH TCGA-A7-A0DC TCGA-A7-A13F 
       25.22        27.12        44.88        21.67        29.79        25.15 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 
       17.98        29.03        31.00        26.01         1.02         9.01 
TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09A TCGA-A8-A09K 
        9.99        36.95        19.96        33.01         9.99        29.98 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A4 TCGA-AN-A04A 
       33.07         8.98         0.99        14.01        13.02         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FS 
        9.96         7.36         0.16         0.33         6.44         6.90 
TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JB 
       81.63        95.70        21.40        20.32        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 
       50.86        72.00        26.24        50.24        62.04       108.72 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TT TCGA-AR-A0TV 
       98.27        57.30        41.62        40.57       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-B6-A0IB TCGA-B6-A0RG 
       98.93        55.86       134.14        93.90       129.57        68.45 
TCGA-BH-A0B4 TCGA-BH-A0BF TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ 
       39.16        43.53        74.14        53.95        49.94        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0E2 
       41.75        89.06        90.97        45.83        13.91        14.30 
TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HU 
       53.26        41.00        52.96         5.85         2.37        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18S TCGA-C8-A12M 
       51.32        27.25        26.66        30.28        66.05        11.77 
TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A138 TCGA-D8-A13Y 
       12.66        12.66        12.66         3.16         4.08        56.81 
TCGA-D8-A140 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10E TCGA-E2-A14S TCGA-E2-A14V 
       13.25        34.42        46.59        28.44        33.17        34.26 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       32.02        21.04        23.34         9.04        20.58        11.05 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       56.94        14.07        51.39 

$subtype6
TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A07I 
      101.98        56.81        63.29        17.13        21.90        14.01 
TCGA-A8-A08J TCGA-A8-A08X TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AN-A0FT TCGA-AN-A0FV 
       37.05        43.00        45.07         0.99         7.04         0.33 
TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A1AT TCGA-B6-A0I9 
       76.77        64.04        98.33        64.83        41.82        12.13 
TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A18R TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12Z 
       84.13        31.00        37.55        11.93        12.66        12.56 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-E2-A14P TCGA-E2-A14Y TCGA-E2-A152 
        1.87        12.92         4.11        40.96        69.34        69.96 
TCGA-E2-A15H 
       12.92 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.30     0.33     0.33     0.23     0.16     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  129.70   165.76   282.90   263.28   134.14   101.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  37.250   32.745   33.730   43.000   32.020   37.050 
[1] "0.3 - 129.7 (37.2)" "0.3 - 165.8 (32.7)" "0.3 - 282.9 (33.7)"
[4] "0.2 - 263.3 (43.0)" "0.2 - 134.1 (32.0)" "0.3 - 102.0 (37.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       9        7        0        21        12          5          5
  subtype2       7        5        0        17         8          8          2
  subtype3       5        5        0        43        21         11          1
  subtype4       5        6        2        10        12         12          1
  subtype5       9        6        0        34        34         22          4
  subtype6       1        0        0        10        10          4          0
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1          0        2       3
  subtype2          2        0       0
  subtype3          3        2       0
  subtype4          1        3       2
  subtype5          4        4       1
  subtype6          5        2       0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           9        7        5        5        9        1
  STAGE IA          7        5        5        6        6        0
  STAGE IB          0        0        0        2        0        0
  STAGE IIA        21       17       43       10       34       10
  STAGE IIB        12        8       21       12       34       10
  STAGE IIIA        5        8       11       12       22        4
  STAGE IIIB        5        2        1        1        4        0
  STAGE IIIC        0        2        3        1        4        5
  STAGE IV          2        0        2        3        4        2
  STAGE X           3        0        0        2        1        0
[1] 10  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 21 33  3  6
  subtype2 16 24  7  2
  subtype3 14 68 10  1
  subtype4 18 25  7  4
  subtype5 20 77 18  3
  subtype6  5 20  5  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       21       16       14       18       20        5
  T2       33       24       68       25       77       20
  T3        3        7       10        7       18        5
  T4        6        2        1        4        3        2
[1] 4 6
[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
  subtype1 35 19  5  3
  subtype2 26 14  6  2
  subtype3 53 26 10  4
  subtype4 21 18 11  3
  subtype5 51 42 16  7
  subtype6  8 14  3  6
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       35       26       53       21       51        8
  N1       19       14       26       18       42       14
  N2        5        6       10       11       16        3
  N3        3        2        4        3        7        6
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1  58   2
  subtype2  49   0
  subtype3  89   3
  subtype4  47   4
  subtype5 114   4
  subtype6  30   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    2
  subtype2   49    0
  subtype3   89    3
  subtype4   47    4
  subtype5  114    4
  subtype6   30    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       58       49       89       47      114       30
  1        2        0        3        4        4        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  63   1
  subtype2  49   0
  subtype3  93   0
  subtype4  54   0
  subtype5 114   4
  subtype6  32   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    1
  subtype2   49    0
  subtype3   93    0
  subtype4   54    0
  subtype5  114    4
  subtype6   32    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       63       49       93       54      114       32
  MALE          1        0        0        0        4        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 26 30
  subtype2 14 25
  subtype3 33 50
  subtype4 17 28
  subtype5 56 41
  subtype6 15 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   30
  subtype2   14   25
  subtype3   33   50
  subtype4   17   28
  subtype5   56   41
  subtype6   15   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        26       14       33       17       56       15
  YES       30       25       50       28       41       14
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            59                              1
  subtype2                            39                              9
  subtype3                            86                              0
  subtype4                            43                              8
  subtype5                            98                             11
  subtype6                            29                              2
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                3
  subtype2                   0                                1
  subtype3                   1                                0
  subtype4                   0                                2
  subtype5                   0                                1
  subtype6                   0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              0
  subtype3                  0              6
  subtype4                  0              1
  subtype5                  2              6
  subtype6                  0              1
D6V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          59       39       86       43       98
  INFILTRATING LOBULAR CARCINOMA          1        9        0        8       11
  MEDULLARY CARCINOMA                     0        0        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        1        0        2        1
  MUCINOUS CARCINOMA                      0        0        0        0        2
  OTHER  SPECIFY                          1        0        6        1        6
                                  clus
vv                                 subtype6
  INFILTRATING DUCTAL CARCINOMA          29
  INFILTRATING LOBULAR CARCINOMA          2
  MEDULLARY CARCINOMA                     0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          1
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         4
  subtype2                                0     1                         1
  subtype3                                0     7                        13
  subtype4                                0     0                         3
  subtype5                                0    10                         7
  subtype6                                1     6                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    44
  subtype3    65
  subtype4    44
  subtype5    79
  subtype6    17
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   3        1        7        0       10
  BLACK OR AFRICAN AMERICAN               4        1       13        3        7
  WHITE                                  46       44       65       44       79
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                   6
  BLACK OR AFRICAN AMERICAN               1
  WHITE                                  17
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
          cls
clus        0  1
  subtype1  1 47
  subtype2  0 36
  subtype3  1 77
  subtype4  2 36
  subtype5  2 78
  subtype6  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   47
  subtype2    0   36
  subtype3    1   77
  subtype4    2   36
  subtype5    2   78
  subtype6    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        1        2        2        0
  NOT HISPANIC OR LATINO       47       36       77       36       78       24
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 480  76
  subtype2 256  51
  subtype3 191  23
subtype1 subtype2 subtype3 
     556      307      214 
subtype1 subtype2 subtype3 
      76       51       23 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14        42.81        40.14        11.44        48.36         9.96 
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       14.27        20.88         7.96        39.32        18.21       143.15 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT 
      121.94        63.12        36.13        88.60        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER 
        5.19       107.93        61.58        25.22       101.72        74.40 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV 
       35.05        34.29        31.82        63.29        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD 
       44.88        49.84        20.52        17.46        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       50.47        21.67        49.48        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KD 
       60.72        19.56        42.44        17.19       105.34        39.65 
TCGA-A2-A4RW TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
        7.30        23.21        21.14        38.30        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J 
       37.45        25.15        23.61        31.36        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SB 
       22.32        11.34        10.59        10.29        13.41        13.74 
TCGA-A7-A4SF TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T 
       17.92        10.42        13.02        13.02         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       18.97        18.97        14.01        12.00        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       33.01       112.08        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 
        8.98        19.04        15.02         0.99        12.00        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 
       27.02        17.03        38.04         0.95        22.95         1.48 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A3EH TCGA-AC-A3QQ TCGA-AC-A3TM 
       99.35        26.04        19.33         6.48        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XS TCGA-AC-A5XU 
       14.99        19.79        24.79        29.26        19.33        14.96 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X 
       11.44        17.42         1.68         8.22         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ 
        0.33         0.23         0.33         0.62         2.96         9.96 
TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW 
        7.36         6.44         5.65         7.00         7.04         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        80.28        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 
       95.70        47.87        29.13        21.40        26.04        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       22.36        21.53        50.24        71.80        99.25       108.72 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ 
       98.27        65.56        41.62        40.57        82.62        61.87 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
        0.53        17.79        24.79         5.65        15.62        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       32.91        19.20        98.33         5.26       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AN 
       98.93        55.86       107.24        83.87       134.14        96.00 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K 
       93.90        37.81        61.28        86.53       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       94.22       120.33        99.78         2.76       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LE TCGA-AR-A2LK 
      105.30        98.76        98.66        89.00       166.42        54.21 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0I8 TCGA-B6-A0IA TCGA-B6-A0IB 
       66.15        73.35       281.29        24.62       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG 
       50.70       146.50       127.33        84.59       165.76        68.45 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        79.63        18.35       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       28.27        68.94        43.59        73.51       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0B0 
       68.12       103.63        71.15        62.93        25.55        81.44 
TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B8 TCGA-BH-A0BD 
       37.74        39.16        70.22        81.63        51.58        18.21 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0C7 
       76.60        53.95        45.57        49.94        44.02        90.97 
TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.83        38.01         3.22         2.56        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 
       44.81        24.49        24.43        10.78        15.16        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL 
       23.08        41.00        52.96        26.50        20.38         2.37 
TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
       16.96         2.50        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       50.79        23.93        44.81        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO 
       26.66        37.74        30.28        66.05        51.39        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 
      113.82        82.85        12.00        55.69        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
       89.16        24.62        33.17       122.89        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       45.63       144.59        83.31         6.44        20.12        10.52 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       23.51         9.63         9.70        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A138 
       12.66        12.66        12.66        48.53         3.16         4.08 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO 
       12.33        11.34        11.28        10.42        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A 
       20.25        12.53         8.28         9.67         9.53        24.56 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1JC TCGA-D8-A1JD 
       12.95        12.49        13.25        20.58        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.90        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV 
       19.92        55.30        15.85        16.31        12.99        15.16 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.54        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.45        16.41         4.80        10.09        13.08        12.26 
TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A106 
       18.51        16.18        12.66        25.22        43.00        83.54 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       28.87        44.68        33.17        75.98        34.26        32.02 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        9.04        20.58        50.79        56.94        14.07        51.39 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       33.01        16.47        37.25        77.65        70.36        33.73 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 
       59.18         3.88        22.19        11.08        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 
       19.66        24.59        26.99        34.55         8.28        30.61 
TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA 
       39.72        34.29        34.82        32.88        36.82        36.56 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.24        25.84        18.94         9.86        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        21.27        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       41.03        41.72        40.50        38.99         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y 
       12.33        29.72        38.07        32.91        23.90        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        26.40        27.85        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        16.57        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA 
       40.41        41.13        52.96        23.11        18.48        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       13.94        10.52        14.43        22.09        34.03        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 
       23.51        15.22        16.77        31.30         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       83.34        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NY TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A442 TCGA-LL-A50Y 
       38.20        18.12        11.57        21.24        29.23        25.05 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 
       15.32        14.70        22.26         2.63        19.53        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66H TCGA-OL-A66K 
       17.49        27.91        31.99        58.62        26.70        41.92 
TCGA-OL-A66O TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       17.36        40.11         8.91        47.01        64.21         0.16 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA17 
       18.81        18.48        21.07        13.84        18.87        13.94 
TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-WT-AB44 TCGA-Z7-A8R6 
       66.84        52.96        29.03       107.05 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      131.67         8.52        31.79        28.01        19.20        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CM 
       78.41        73.84        87.25       101.98        55.43        24.79 
TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ 
       56.81        55.00        67.33        34.55        33.76        79.76 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T7 
       99.19        50.43        17.52        17.13         8.38        20.75 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F 
       18.21        21.90        18.61        31.73        19.20        10.59 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        91.07        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 
       35.93        50.37        50.83        24.39        26.96        21.90 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G 
       35.31        35.67        31.73        20.19        24.26        23.74 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV 
       21.73        14.50        21.17        14.73        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A07B TCGA-A8-A07C 
        9.37         8.75        17.98        29.03        43.00        33.99 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P 
        9.99         8.98        24.99        38.01         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A23H TCGA-AC-A2BK 
        0.99        43.00        14.01         0.99         5.72        73.05 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A5EH TCGA-AC-A62X TCGA-AC-A6IW 
       33.04        14.66        16.57        16.80        13.71        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM 
        0.03         1.12         1.78         1.71         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FV 
        0.33         0.33         0.33         7.96         7.59         0.33 
TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03U 
        0.33         0.53         0.33         0.33        61.35        58.95 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL 
       32.78        52.18        37.48        72.00        76.77        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR 
      115.27       106.78       108.03        64.04        48.36        70.39 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
       26.93       130.09         2.56       140.55        84.10        23.31 
TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       64.83        65.36       107.21       125.16       108.36       101.00 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24U 
       99.32        17.23        41.82        33.73       104.28        77.69 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 
       99.62        85.64        93.83        57.27        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ 
      143.38        32.58        12.13       233.62        18.77       140.88 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX 
      255.68       212.25       100.70        89.46       282.90        21.47 
TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 
      245.10       101.52       139.17        37.87         7.07        70.16 
TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0B9 
       18.84        59.84        20.45        39.55        84.13        51.68 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       43.53        61.51        74.89        77.95        49.05        41.75 
TCGA-BH-A0DL TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY 
       78.28        16.27         4.41         9.63        31.00        30.35 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
        5.59        23.05         4.90        55.63        37.55         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC 
       51.16        67.50        49.58        25.81        97.48       114.15 
TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07        72.07        26.14        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
       18.64         5.26        11.93        11.77        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y 
       10.92         0.16        12.03        12.33        12.36        12.95 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         9.50        14.43        13.02        56.81        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        19.20        14.17        17.49        16.50 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XJ 
       12.03        53.00        20.12        20.09        19.40        21.80 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1Y3 TCGA-D8-A27F 
       14.50        16.41        16.64        43.04        14.14        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14X 
       13.05        13.48        47.15        40.96        38.60        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       69.34        63.62        69.96        14.79        25.05        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       53.62        28.50        33.70        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A573 
      106.75       102.61         8.75        43.04        52.73        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       38.76        17.69        22.29        34.16        36.20        39.55 
TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.62        46.59        40.73        20.12         0.69         1.94 
TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
       30.18         0.79        25.94        22.82        29.82         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SB 
       19.99         6.15        19.96        55.00        17.49        24.99 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       33.21       109.87        79.10        75.02        70.85        72.10 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO 
       69.30         2.60        11.84        10.62        17.06        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A8F5 TCGA-OL-A5D6 
       14.79        16.08        15.68        14.50        19.59        36.30 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       58.52        36.36        24.72        22.32        20.38        23.47 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UL-AAZ6 
       14.07        28.21         9.93        20.68        19.27        17.03 
TCGA-UU-A93S 
        3.81 

$subtype3
TCGA-5L-AAT0 TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SJ 
       48.56        14.37        43.43        48.10        47.24        13.68 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CV 
      136.73        99.12       114.81        92.48       107.93        98.99 
TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW 
       53.13        89.36        80.28       118.45        72.00        61.94 
TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T6 TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ 
       24.72        44.28        18.90        19.33        48.46        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC 
       20.25        16.47        52.47       107.70        18.15        36.23 
TCGA-A2-A4RY TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A3J1 TCGA-A7-A425 
       21.30        34.29        33.11        29.56        11.28        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E 
       11.97        14.93        14.66        10.72        11.05        19.99 
TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB 
       31.00         9.99        13.02        21.04        73.91        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A3BB 
       86.66        90.71        60.92        87.12        74.14        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A6IV 
       16.31        14.83        22.19        15.48        23.24        18.67 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
       12.26        20.19         2.30         7.17         6.90         5.36 
TCGA-AO-A03R TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG 
       68.75        53.03        50.70        50.86        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KO TCGA-AR-A1AK TCGA-AR-A1AL 
       62.04        90.58        57.30        14.73       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24T 
       98.33        86.07        94.29        86.43       118.59       105.27 
TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       32.58        93.30        71.05        20.25        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IE 
       38.17        39.39        40.54        33.30        38.96        65.72 
TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-B6-A0X7 
      112.37       129.07       140.48       157.41       113.79        58.88 
TCGA-BH-A0AZ TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       63.09        37.22        32.02        21.70        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       75.48        74.14        89.06        77.98        23.44        29.98 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       13.91        17.26        15.65        38.47        67.86        70.88 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HF TCGA-BH-A0HK 
       46.19        32.58        37.78        53.26        23.90         5.85 
TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EU 
       13.61        24.95        42.35        32.91        72.56        42.28 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U 
      120.62        74.73        36.92        28.14        10.65       109.28 
TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A3M7 TCGA-C8-A8HR 
       20.88        18.87        21.76         9.44        33.99        13.41 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1XM 
       13.48        21.14        55.50        14.01        14.70        17.69 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
       14.43        48.03         1.61        12.53        33.37        21.67 
TCGA-E2-A108 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14Z TCGA-E2-A15E TCGA-E2-A15M 
       27.52        38.24        43.33        18.51        20.71        11.05 
TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO 
       19.56        87.22        32.35        37.41        28.44        60.99 
TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A2JT 
       54.18        43.56        35.77        24.82        28.27         9.47 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 
       30.44        26.70        12.20        13.25        39.78        30.08 
TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A3NW 
       34.55        52.73        25.91       216.76        85.15       110.50 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LD-A74U 
       43.73        66.38        72.03        13.55        62.47        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A73Z TCGA-MS-A51U 
        7.10        13.28        24.95        32.75         7.46        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66J TCGA-OL-A66L 
        2.10        40.08        34.92        28.87        65.62        42.77 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DE TCGA-PL-A8LY TCGA-S3-AA14 TCGA-S3-AA15 
       26.04        19.73        86.96         0.26        17.39        17.26 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        15.35        16.04       108.07 

subtype1 subtype2 subtype3 
    0.16     0.03     0.26 
subtype1 subtype2 subtype3 
  281.29   282.90   216.76 
subtype1 subtype2 subtype3 
  25.415   26.930   34.140 
[1] "0.2 - 281.3 (25.4)" "0.0 - 282.9 (26.9)" "0.3 - 216.8 (34.1)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      46       44        5        2       178       129         1
  subtype2      19       22        0        2       132        73         0
  subtype3      24       21        1        2        49        53         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         93         22         24       12         0      10
  subtype2         33          6         14        5         0       1
  subtype3         29          1         27        3         1       3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          46       19       24
  STAGE IA         44       22       21
  STAGE IB          5        0        1
  STAGE II          2        2        2
  STAGE IIA       178      132       49
  STAGE IIB       129       73       53
  STAGE III         1        0        1
  STAGE IIIA       93       33       29
  STAGE IIIB       22        6        1
  STAGE IIIC       24       14       27
  STAGE IV         12        5        3
  STAGE TIS         0        0        1
  STAGE X          10        1        3
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1 148 326  64  27
  subtype2  65 206  28  11
  subtype3  67 100  45   2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      148       65       67
  T2      326      206      100
  T3       64       28       45
  T4       27       11        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 253 194  76  31
  subtype2 168  95  28  16
  subtype3  94  72  16  30
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      253      168       94
  N1      194       95       72
  N2       76       28       16
  N3       31       16       30
[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"
D7V6, binary
          cls
clus         0   1
  subtype1 473  13
  subtype2 266   6
  subtype3 163   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  473   13
  subtype2  266    6
  subtype3  163    3
   clus
vv  subtype1 subtype2 subtype3
  0      473      266      163
  1       13        6        3
[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"
D7V7, binary
          cls
clus         0   1
  subtype1 555  12
  subtype2 311   0
  subtype3 215   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  555   12
  subtype2  311    0
  subtype3  215    0
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      555      311      215
  MALE         12        0        0
[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"
D7V8, binary
          cls
clus         0   1
  subtype1 233 263
  subtype2 129 142
  subtype3  73 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  233  263
  subtype2  129  142
  subtype3   73  118
     clus
vv    subtype1 subtype2 subtype3
  NO       233      129       73
  YES      263      142      118
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           414
  subtype2                          1                           271
  subtype3                          0                            98
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             90                   0
  subtype2                              8                   6
  subtype3                            104                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               17
  subtype2                     9                                3
  subtype3                     0                                8
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                 17             29
  subtype2                  0             12
  subtype3                  0              5
D7V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              0        1        0
  INFILTRATING DUCTAL CARCINOMA         414      271       98
  INFILTRATING LOBULAR CARCINOMA         90        8      104
  MEDULLARY CARCINOMA                     0        6        0
  METAPLASTIC CARCINOMA                   0        9        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       17        3        8
  MUCINOUS CARCINOMA                     17        0        0
  OTHER  SPECIFY                         29       12        5
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    33                        71
  subtype2                                1    23                        89
  subtype3                                0     5                        23
          vv
clus       WHITE
  subtype1   396
  subtype2   178
  subtype3   179
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  33       23        5
  BLACK OR AFRICAN AMERICAN              71       89       23
  WHITE                                 396      178      179
[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"
D7V12, binary
          cls
clus         0   1
  subtype1  25 439
  subtype2   7 261
  subtype3   7 180
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25  439
  subtype2    7  261
  subtype3    7  180
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           25        7        7
  NOT HISPANIC OR LATINO      439      261      180
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 246  41
  subtype2 128  35
  subtype3  82   9
  subtype4 266  26
  subtype5 159  27
  subtype6  46  12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     287      163       91      292      186       58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      41       35        9       26       27       12 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SQ TCGA-A2-A04N 
      129.14        42.81         9.96        14.27        18.21       143.15 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0ER TCGA-A2-A0ET 
      121.94        63.12        88.60        77.19        74.40        35.05 
TCGA-A2-A0SU TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 
       54.64        32.55        50.47        17.36        60.72        19.56 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A4S0 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13F 
       17.19       105.34        23.21        38.30        30.61        25.15 
TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.61        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.41        13.02        13.02        53.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z 
        1.02         9.01        32.05        10.98         7.99        45.07 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08Z 
       36.95        13.02         0.99        28.96        19.96        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E 
       33.01        17.95         9.99        12.00         1.02        49.05 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A9 TCGA-A8-A0AD 
       29.98        33.07        25.02        19.04        27.02        38.04 
TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3TN TCGA-AC-A3YJ TCGA-AC-A5XU 
       22.95        99.35        26.04        14.99        24.79        14.96 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
       11.44        17.42         8.22         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FY 
        0.23         2.96         6.44         5.65         7.00         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33         0.30         0.33        95.70        21.40        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JI TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C 
       22.36        50.24        99.25       108.72        98.27        65.56 
TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       40.57        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       15.62        32.91         5.26        75.22        55.86       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24L 
       83.87       134.14        37.81        61.28        50.89        94.22 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0IA 
      112.77       105.30        98.66        54.21        66.15       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RI TCGA-B6-A0RL 
      129.57        50.70       127.33       165.76       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X4 
       78.02       102.77       188.68        79.63       206.86        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-BH-A0AU TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD 
       68.94        43.59        62.93        49.94        90.97        45.83 
TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H6 
       15.68        44.81        24.49        24.43        15.16        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO 
       41.00        52.96        20.38         2.37        16.96         2.50 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES 
       51.32        23.93        26.66        37.74        66.05       113.82 
TCGA-BH-A1F5 TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A204 
       89.16        33.17       122.89        63.35       144.59        83.31 
TCGA-BH-A42T TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X 
       10.52         9.63         9.70        11.77        11.77        12.66 
TCGA-C8-A12Y TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN 
       48.53        12.33        11.34        11.28        10.42        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 
       12.33        20.25         8.28         9.67        24.56        12.95 
TCGA-D8-A140 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1JT 
       13.25        18.15        18.90        18.97        12.20        13.32 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        17.79        16.73        27.58        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       15.22        14.73        55.30        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1Y1 TCGA-D8-A27E TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A105 
       15.16         9.93        17.42        12.26        12.66        43.00 
TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14S 
       83.54        46.59        40.41        37.51        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       75.98        32.02        23.24        19.43        21.04        23.87 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        12.92        53.92         9.04        20.58 
TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1IG 
       50.79        56.94        14.07        51.39        33.01        70.36 
TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       59.18        22.19        60.36        73.64        19.66        24.59 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 
        8.28        30.61        39.72        34.29        34.82        36.82 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       25.84        18.94         9.86         2.56         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI 
       48.23        40.24         1.12        46.65        21.27        47.64 
TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A247 
       34.45        42.25        37.74        38.37        40.50        38.99 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y 
       24.56        29.72        38.07        32.91        23.90        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 
       25.81        26.40        18.90        28.77        29.95        41.13 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW 
       23.11        18.48        18.90        10.52        52.73        22.09 
TCGA-EW-A6SA TCGA-GM-A2DC TCGA-GM-A2DM TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM 
       16.77        83.34       106.06        29.23        25.05        15.32 
TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A66H TCGA-OL-A66O TCGA-PE-A5DC 
        2.63        12.36        31.99        26.70        17.36        47.01 
TCGA-PL-A8LX TCGA-S3-AA11 TCGA-S3-AA12 TCGA-V7-A7HQ TCGA-Z7-A8R6 
        0.16        13.84        18.87        66.84       107.05 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W 
      131.67        20.88        31.79         7.96        39.32       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D1 
       55.43        36.13       107.93        56.81        55.00        34.55 
TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       31.82        27.12        44.88        21.90        21.67        23.77 
TCGA-A2-A25B TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26H TCGA-A7-A4SF TCGA-A7-A56D 
       42.44        26.96        21.90        23.80        17.92        14.73 
TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       10.42         1.02        17.98        31.00        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B 
       43.00        18.97        14.01         9.99        15.06        38.01 
TCGA-A8-A08F TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       33.01        37.05         9.99        31.00        33.01       112.08 
TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09W 
       30.97        12.00        45.07         1.02         8.98         0.99 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AC-A7VC 
        0.95         5.72        33.04         6.48        16.80         0.03 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV 
        9.96         7.36         0.16         0.33         7.04         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JM 
        0.33        12.33         5.59        66.77        81.63        71.80 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TW TCGA-AR-A1AT TCGA-AR-A24H TCGA-AR-A250 
      130.09         5.65        98.93        41.82       160.90        89.00 
TCGA-AR-A254 TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RH TCGA-B6-A0RO 
       85.64        24.62        12.13       146.50       212.25       162.05 
TCGA-B6-A0WW TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B4 TCGA-BH-A0BR 
       18.35       139.17        68.12       103.63        39.16        76.60 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0H7 TCGA-BH-A0HU 
       45.57        49.05        44.02        16.27        23.08        12.89 
TCGA-BH-A0HY TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18U TCGA-BH-A1EN 
       50.79        20.12        90.84        30.28        51.39        67.50 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM 
       12.00        49.58        17.69        31.53        24.62        45.63 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z 
       72.07        26.14        12.66        12.66        12.66        12.56 
TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-C8-A274 
        3.16         4.11         4.08        10.92        12.33         9.53 
TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       12.49        56.81        14.17        17.49        16.50        15.78 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XY 
       20.09        20.38        21.01        23.90        21.80        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27N TCGA-D8-A27R TCGA-E2-A107 TCGA-E2-A10C 
       15.32        14.14         4.80        10.09        34.42        40.11 
TCGA-E2-A10E TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A2P5 TCGA-E2-A9RU 
       28.44        34.26        69.96        23.34        26.99        17.69 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A1RB 
       22.29        36.20        36.56        35.24         6.12        32.09 
TCGA-E9-A1RF TCGA-E9-A22A TCGA-E9-A22E TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A2FR 
        6.58        39.09        41.72        29.85         6.15        55.00 
TCGA-EW-A423 TCGA-EW-A6S9 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-JL-A3YX TCGA-LL-A6FP 
       10.16        15.22         7.40        59.57        11.57        22.26 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-OL-A97C TCGA-S3-A6ZF TCGA-UL-AAZ6 
       17.49        27.91        22.32         8.91        18.81        17.03 
TCGA-WT-AB44 
       29.03 

$subtype3
TCGA-3C-AALK TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       40.14        43.43        47.24       114.81        92.48       107.93 
TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0YK 
       53.13        80.28        72.00        61.94        24.72        19.33 
TCGA-A2-A0YL TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A7-A0CG 
       48.46        16.47       107.70        39.65        21.30        34.29 
TCGA-A7-A13H TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A0A4 TCGA-AC-A23G 
       29.56        11.97        10.72        11.05        13.02        73.91 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3W7 
       90.71        60.92        87.12        16.31        22.19        15.48 
TCGA-AC-A3YI TCGA-AC-A8OS TCGA-AO-A0JB TCGA-AO-A0JJ TCGA-AO-A1KO TCGA-AR-A1AL 
       23.24         2.30        50.70        62.04        14.73        97.68 
TCGA-AR-A1AM TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LM TCGA-AR-A2LN 
       98.33       118.59       105.27        32.58        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RV 
       40.54        38.96       112.37       129.07       140.48       157.41 
TCGA-BH-A0AZ TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0DO 
       63.09        37.22        21.70        61.68        72.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0E9 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A18M TCGA-BH-A1FH 
       15.65        46.19        13.61        24.95        72.56        36.92 
TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-A8G0 
       28.14        10.65       109.28        20.88        18.87        21.76 
TCGA-C8-A3M7 TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E 
       33.99        33.37        21.67        38.24        43.33        20.71 
TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1L6 TCGA-EW-A1J2 TCGA-EW-A1PG TCGA-GM-A3XG 
       37.41        28.44        54.18        13.25        34.55        43.73 
TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-MS-A51U 
       13.55        62.47        13.22        13.28        24.95        22.39 
TCGA-OL-A5RV TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY TCGA-S3-AA14 TCGA-W8-A86G 
       34.92        19.73        40.11         0.26        17.39        11.41 
TCGA-Z7-A8R5 
      108.07 

$subtype4
TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SJ 
       11.44        48.56        48.36        14.37        48.10        13.68 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D3 
      136.73        99.12        75.25         5.19        98.99        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0EU 
       25.22       101.72        89.36       118.45        79.76        34.29 
TCGA-A2-A0SY TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       44.28        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YD TCGA-A2-A0YI TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A259 
       25.28        49.48        23.47        22.45        20.25        52.47 
TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4S2 
       18.15        36.23        56.28        50.37         7.30        21.14 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A425 
       35.47        37.45        33.11        31.36        11.28        14.70 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07J 
       14.93        13.74        14.66        19.99        18.97        12.00 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09V 
       12.00        31.00        41.98         9.99        50.04        15.02 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A2B8 TCGA-AC-A2FB 
       12.00        19.04        21.04        17.03         1.48        40.57 
TCGA-AC-A2FE TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QQ 
       86.66        74.14        19.33        32.45        14.83        24.13 
TCGA-AC-A3TM TCGA-AC-A3W6 TCGA-AC-A4ZE TCGA-AC-A5XS TCGA-AC-A6IV TCGA-AC-A6IX 
       25.05        19.79        29.26        19.33        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A0FN TCGA-AN-A0FS 
        1.68        20.19         0.33         0.62         7.17         6.90 
TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L 
        0.36         5.36         0.33         0.33         5.33        80.28 
TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J9 
       61.35        68.75        47.87        29.13        26.04        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A12A 
       21.53        50.86        72.00        65.10        26.24        90.58 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT 
       57.30        41.62        32.52        19.20        98.33       109.02 
TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
      103.86        96.00        93.90        94.29        86.53        86.43 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24X TCGA-AR-A252 
      120.33        99.78         2.76        97.84        98.76        93.30 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QN 
       71.05       166.42        86.53        39.39        73.35        33.30 
TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IN TCGA-B6-A0RG TCGA-B6-A0RN TCGA-B6-A0WS 
      281.29        65.72        84.59        68.45       263.28        97.48 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
      113.79       129.70        58.88        73.51       170.17        85.35 
TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B5 TCGA-BH-A0B6 
       71.15        25.55        81.44        37.74        70.22        81.63 
TCGA-BH-A0B8 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BP TCGA-BH-A0BQ 
       51.58        32.02        18.21        43.53        75.48        74.14 
TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       53.95        41.75        89.06        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       29.98        13.91         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0E2 TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       70.88        14.30        32.58        30.35        10.78        37.78 
TCGA-BH-A0H5 TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HQ TCGA-BH-A0HX 
       53.26        26.50        23.90         5.85        36.85        27.25 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18R TCGA-BH-A1EO 
       42.35        44.81        32.91        35.93        37.55        91.99 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FL 
       82.85        42.28        55.69       120.62        74.73        55.00 
TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A5J0 TCGA-BH-AB28 TCGA-C8-A132 
      130.16         6.44        20.12        23.51         9.44         1.87 
TCGA-C8-A26W TCGA-C8-A8HR TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB 
       12.53        13.41        20.58        13.48        21.14        55.50 
TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XL TCGA-D8-A1XM 
       14.01        14.70        25.74        18.15        19.92        17.69 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       15.52        14.24        13.45        14.43        48.03        16.41 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-D8-A73X 
        1.61        13.08        12.53        18.51        16.18        25.22 
TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Z TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15I 
       27.52        28.87        18.51        22.82        17.29        55.63 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
       11.05        19.56        87.22        32.35        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A2P6 
       77.65        33.73         3.88        60.99        11.08        34.55 
TCGA-E2-A3DX TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       43.56        32.88        35.77        24.82        28.27        34.95 
TCGA-E9-A1RA TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JT 
       45.01        32.05        41.03         7.13        12.33         9.47 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       30.44        26.70        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P1 
       18.21        16.57        15.68        25.94        40.41        39.78 
TCGA-EW-A1P3 TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A424 
       52.96        13.94        14.43        25.91        34.03        23.51 
TCGA-EW-A6SC TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       31.30       216.76        72.10        85.15        86.96       115.69 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62        85.35       110.50        38.20        66.38        72.03 
TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A7SZ 
       18.12        21.24         7.10        17.06        14.70        19.53 
TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX TCGA-OL-A66J TCGA-OL-A66K 
        2.10        58.62        40.08        28.87        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-S3-A6ZH 
       42.77        26.04        64.21        86.96        18.48        21.07 
TCGA-S3-AA17 TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       13.94        52.96        15.35        16.04 

$subtype5
TCGA-A1-A0SB TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
        8.52        28.01        19.20        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX 
       87.25        24.79        67.33        33.76        99.19        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
       17.52         8.38        18.21        18.61        31.73        19.20 
TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY 
       10.59        33.93        91.07        29.98        47.31        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       50.83        24.39        35.31        35.67        31.73        20.19 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       24.26        23.74        21.73        14.50        21.17        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R 
       10.29         9.37         8.75        33.99         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW 
       24.99         0.99        73.05        14.66        13.71        13.58 
TCGA-AC-A8OQ TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        1.12         1.71         7.46         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 
        7.59         0.33         0.53         0.33        58.95        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F 
       37.48        55.33       115.27       106.78       108.03        48.36 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
       70.39        26.93         2.56       140.55        84.10        23.31 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       65.36       107.21       125.16       108.36       101.00        99.32 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR 
       17.23        33.73       104.28        99.62        93.83        57.27 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       10.59        77.62       143.38        32.58       233.62       140.88 
TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      255.68        89.46       282.90        21.47       245.10       101.52 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 
       37.87         7.07        70.16        18.84        59.84        39.55 
TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 
       51.68        61.51        74.89        77.95        78.28         4.41 
TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T 
        9.63         5.59        23.05         4.90        55.63         7.36 
TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A5IZ TCGA-BH-A6R9 
       51.16        25.81        97.48       114.15        18.64         5.26 
TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 
       12.66        12.59         0.16        14.43        13.97        19.20 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F 
       20.09        19.40        14.50        16.41        43.04        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       13.05        13.48        47.15        38.60        31.96        69.34 
TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II 
       63.62        14.79        25.05        76.57        28.50        33.70 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS 
       50.07       106.75       102.61         8.75        43.04        52.73 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A22G 
       34.92        38.76        34.16        39.55        41.62        40.73 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 
       20.12         0.69        30.18         0.79        22.82        29.82 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-EW-A6SB 
       30.08         7.86        19.99        19.96        17.49        24.99 
TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A5YP 
      109.87        70.85        69.30         2.60        32.75        14.79 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 
       16.08        15.68        19.59        58.52        36.36        20.38 
TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       23.47        28.21         9.93        20.68        19.27        17.26 

$subtype6
TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A3XV TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 
       63.29        17.13        32.75        43.00        14.01         0.99 
TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AO-A0J2 TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TX 
       16.57         1.78        32.78        76.77        64.04        64.83 
TCGA-AR-A1AO TCGA-AR-A24U TCGA-AR-A2LH TCGA-B6-A0IK TCGA-B6-A0RS TCGA-BH-A0AW 
       86.07        77.69        20.25        18.77       100.70        20.45 
TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L 
       84.13        31.00        72.07        38.60        57.83        11.93 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HK TCGA-C8-A26X 
       11.77        12.66        13.51        12.92        12.03        12.36 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A143 
       12.95         0.03         9.50        13.02        20.88        14.17 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT TCGA-E2-A14P TCGA-E2-A1B0 
       12.03        53.00        20.12        16.64        40.96        53.62 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E9-A1RH TCGA-E9-A248 TCGA-EW-A6SD TCGA-GM-A2DB 
       75.81        28.90        46.59         1.94        33.21        79.10 
TCGA-GM-A2DD TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 
       75.02        11.84        10.62        14.47         7.46        14.50 
TCGA-OL-A5D6 TCGA-OL-A5RY TCGA-OL-A66P TCGA-UU-A93S 
       36.30        24.72        14.07         3.81 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.16     0.03     0.26     0.33     0.16     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  275.87   212.25   157.41   281.29   282.90   100.70 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  25.150   23.080   37.220   32.200   28.355   20.185 
[1] "0.2 - 275.9 (25.1)" "0.0 - 212.2 (23.1)" "0.3 - 157.4 (37.2)"
[4] "0.3 - 281.3 (32.2)" "0.2 - 282.9 (28.4)" "0.0 - 100.7 (20.2)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      20       23        4        2        95        74         1
  subtype2       7        8        0        1        51        38         0
  subtype3       7       10        1        1        17        27         0
  subtype4      41       26        1        1        87        62         0
  subtype5      13       15        0        1        86        41         0
  subtype6       1        5        0        0        23        13         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         43         15          7        4         0       6
  subtype2         31          8         12        7         0       2
  subtype3         14          1         12        1         0       0
  subtype4         43          0         23        3         1       5
  subtype5         17          4          5        3         0       1
  subtype6          7          1          6        2         0       0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          20        7        7       41       13        1
  STAGE IA         23        8       10       26       15        5
  STAGE IB          4        0        1        1        0        0
  STAGE II          2        1        1        1        1        0
  STAGE IIA        95       51       17       87       86       23
  STAGE IIB        74       38       27       62       41       13
  STAGE III         1        0        0        0        0        1
  STAGE IIIA       43       31       14       43       17        7
  STAGE IIIB       15        8        1        0        4        1
  STAGE IIIC        7       12       12       23        5        6
  STAGE IV          4        7        1        3        3        2
  STAGE TIS         0        0        0        1        0        0
  STAGE X           6        2        0        5        1        0
[1] 13  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  76 170  28  18
  subtype2  25 110  21  10
  subtype3  26  37  27   1
  subtype4  95 156  40   2
  subtype5  40 124  17   6
  subtype6  18  35   4   3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       76       25       26       95       40       18
  T2      170      110       37      156      124       35
  T3       28       21       27       40       17        4
  T4       18       10        1        2        6        3
[1] 4 6
[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
  subtype1 126 115  33  12
  subtype2  66  48  31  14
  subtype3  38  36   5  12
  subtype4 147  89  29  25
  subtype5 117  51  14   6
  subtype6  21  22   8   8
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0      126       66       38      147      117       21
  N1      115       48       36       89       51       22
  N2       33       31        5       29       14        8
  N3       12       14       12       25        6        8
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1 250   5
  subtype2 134   7
  subtype3  69   1
  subtype4 235   3
  subtype5 162   4
  subtype6  52   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  250    5
  subtype2  134    7
  subtype3   69    1
  subtype4  235    3
  subtype5  162    4
  subtype6   52    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      250      134       69      235      162       52
  1        5        7        1        3        4        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1 285   9
  subtype2 164   2
  subtype3  91   0
  subtype4 293   1
  subtype5 188   0
  subtype6  60   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  285    9
  subtype2  164    2
  subtype3   91    0
  subtype4  293    1
  subtype5  188    0
  subtype6   60    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      285      164       91      293      188       60
  MALE          9        2        0        1        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus         0   1
  subtype1 127 136
  subtype2  68  70
  subtype3  41  39
  subtype4 103 156
  subtype5  70  97
  subtype6  26  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127  136
  subtype2   68   70
  subtype3   41   39
  subtype4  103  156
  subtype5   70   97
  subtype6   26   25
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO       127       68       41      103       70       26
  YES      136       70       39      156       97       25
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           224
  subtype2                          0                           138
  subtype3                          0                            28
  subtype4                          0                           176
  subtype5                          1                           163
  subtype6                          0                            54
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             24                   0
  subtype2                             16                   0
  subtype3                             55                   0
  subtype4                            100                   1
  subtype5                              2                   5
  subtype6                              5                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               10
  subtype2                     3                                4
  subtype3                     0                                5
  subtype4                     0                                7
  subtype5                     5                                2
  subtype6                     1                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                 15             21
  subtype2                  1              4
  subtype3                  1              2
  subtype4                  0             10
  subtype5                  0              9
  subtype6                  0              0
D8V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         224      138       28      176      163
  INFILTRATING LOBULAR CARCINOMA         24       16       55      100        2
  MEDULLARY CARCINOMA                     0        0        0        1        5
  METAPLASTIC CARCINOMA                   0        3        0        0        5
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        4        5        7        2
  MUCINOUS CARCINOMA                     15        1        1        0        0
  OTHER  SPECIFY                         21        4        2       10        9
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          54
  INFILTRATING LOBULAR CARCINOMA          5
  MEDULLARY CARCINOMA                     0
  METAPLASTIC CARCINOMA                   1
  MIXED HISTOLOGY (PLEASE SPECIFY)        0
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          0
[1] 8 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    19                        42
  subtype2                                0    14                        20
  subtype3                                0     3                         9
  subtype4                                0     8                        34
  subtype5                                0     5                        65
  subtype6                                1    12                        13
          vv
clus       WHITE
  subtype1   197
  subtype2   106
  subtype3    77
  subtype4   235
  subtype5   110
  subtype6    28
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                  19       14        3        8        5
  BLACK OR AFRICAN AMERICAN              42       20        9       34       65
  WHITE                                 197      106       77      235      110
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                  12
  BLACK OR AFRICAN AMERICAN              13
  WHITE                                  28
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
          cls
clus         0   1
  subtype1  12 229
  subtype2   3 129
  subtype3   2  77
  subtype4  15 236
  subtype5   6 159
  subtype6   1  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  229
  subtype2    3  129
  subtype3    2   77
  subtype4   15  236
  subtype5    6  159
  subtype6    1   50
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO           12        3        2       15        6        1
  NOT HISPANIC OR LATINO      229      129       77      236      159       50
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 257  47
  subtype2 186  28
  subtype3 237  32
  subtype4 236  39
subtype1 subtype2 subtype3 subtype4 
     304      214      269      275 
subtype1 subtype2 subtype3 subtype4 
      47       28       32       39 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO 
      129.14       131.67        42.81        31.79         7.96        28.01 
TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X 
       19.20        18.02        78.41        73.84        87.25        55.43 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 
       99.12        24.79       107.93        55.00        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SX 
       33.76        25.22        79.76        99.19        27.12        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F 
       17.52         8.38        21.90        31.73        19.20        10.59 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3Y0 
       33.93        91.07        29.98        32.75        47.31        50.83 
TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CJ 
       24.39        23.21        26.96        21.90        35.31        30.61 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A3J0 TCGA-A7-A3RF 
       37.45        31.73        20.19        24.26        10.29        13.41 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       14.50        21.17        17.92        12.10        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C 
        8.75        13.02        17.98        53.98         9.01        33.99 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B 
       32.05         9.99         8.98        24.99         9.99        38.01 
TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A7 
        9.99         0.99        45.07        25.02         8.98         0.99 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A62X 
       73.05        33.04        16.57        16.80        11.44        13.71 
TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
       13.58         1.12         0.33         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.59         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XO TCGA-AN-A0XU TCGA-AO-A03R 
        0.33         0.33         0.53        12.33         0.33        68.75 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0JL 
       32.78        21.40        52.18        37.48        20.32        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
      115.27       108.03        64.04        48.36        61.87        70.39 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       26.93         5.65         2.56       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ 
      109.02        83.87       107.21       125.16       108.36        99.32 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 
       17.23        33.73       160.90       104.28        99.62        93.83 
TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I9 
       57.27        10.59        77.62       143.38        32.58        12.13 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WX 
      233.62       140.88       255.68       100.70        89.46        21.47 
TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      113.79        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY 
       37.87         7.07        70.16        18.84        59.84        25.55 
TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 
       39.55        51.68        61.51        45.57        77.95        41.75 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY 
       45.83        78.28         4.41         9.63        31.00        30.35 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18R 
        5.59        23.05         4.90        26.66        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FJ 
        7.36        51.39        51.16        97.48       114.15        63.35 
TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P 
       72.07        38.60        83.31        18.64        11.93        11.77 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66        12.66        13.51        12.59         4.11 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A275 
        0.16        12.33        12.95        20.25        12.95         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 
        9.50        24.56        14.43        56.81        20.88        13.97 
TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1JL 
       14.17        19.20        16.50        15.78        20.12        20.09 
TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       18.58        15.22        21.80        14.50        19.92        16.41 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H 
       15.16        43.04        15.32        14.14        16.04        13.05 
TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14W TCGA-E2-A14X 
       13.48        10.09        40.96        38.60        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       69.34        18.51        63.62        14.79        25.05        23.34 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LG 
       76.57        53.62        28.50        33.70        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61         8.75        43.04        34.92        38.76 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1RB 
       17.69        34.16        36.20        36.56        41.62        32.09 
TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JS 
       46.59        39.09        40.73        20.12         1.94        29.72 
TCGA-E9-A3QA TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
       30.18         0.79        25.81        22.82        29.82         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SA 
       19.99         6.15        19.96        55.00        17.49        16.77 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
       24.99        33.21       109.87        79.10        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LL-A5YN 
       72.10        85.35        69.30         2.60        11.84        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79        16.08        15.68        19.53        12.36 
TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
       19.59        36.30        58.52        36.36        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-AA0Z 
       23.47        14.07        28.21         8.91         9.93        20.68 
TCGA-S3-AA10 TCGA-S3-AA12 TCGA-UL-AAZ6 TCGA-UU-A93S 
       19.27        18.87        17.03         3.81 

$subtype2
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A2-A0CK TCGA-A2-A0CO 
       40.14        11.44        48.36         8.52       136.73       114.81 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES 
      107.93        98.99        53.13        89.36       118.45        72.00 
TCGA-A2-A0EW TCGA-A2-A0T6 TCGA-A2-A0YK TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A25A 
       61.94        18.90        19.33        20.25        16.47       107.70 
TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       18.15        36.23        39.65        56.28        35.93        50.37 
TCGA-A2-A4RY TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A4SC 
       21.30        29.56        23.74        11.34        11.28        14.66 
TCGA-A7-A5ZW TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       10.72        21.04        73.91        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        74.14        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A6IV 
       19.79        15.48        23.24        29.26        14.53        18.67 
TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AO-A0JF TCGA-AO-A12A 
       12.26         0.03        20.19         2.30        65.10        90.58 
TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TY TCGA-AR-A1AJ 
       57.30        14.73        32.52        19.20        55.86       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX 
      103.86        97.68        98.33        86.07        94.29        86.43 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LE TCGA-AR-A2LH 
      118.59         2.76       105.27        32.58       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0RQ 
       33.30        38.96        65.72       112.37        18.77       140.48 
TCGA-B6-A0RU TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ 
      282.90       170.17        85.35       103.63        71.15        63.09 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE 
       81.63        74.89        72.23        49.05        89.06        77.98 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E9 TCGA-BH-A0EA 
       29.98        17.26        38.47        67.86        46.19        32.58 
TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EO 
       37.78        13.61        24.95        32.91        72.56        91.99 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE 
       42.28        55.69        49.58        25.81       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       36.92        72.07        28.14        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      109.28        20.88         5.26        18.87        21.76         9.44 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       12.53        12.36        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A27I TCGA-D8-A27L 
       13.41        55.50        14.01        14.70        14.43        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A108 
        4.80         1.61        13.08        21.67        16.18        27.52 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A1B1 TCGA-E2-A1BC 
       47.15        38.24        43.33        20.71        87.22        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1L6 TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E9-A1NE 
       37.25        33.73        54.18        26.99        43.56        35.77 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-EW-A1IW 
       24.82        28.27         9.47        32.91        30.44        12.20 
TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PF TCGA-EW-A1PG 
       13.25        39.78        30.08        18.90        14.43        34.55 
TCGA-EW-A2FV TCGA-EW-A6SC TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       25.91        31.30        83.34        85.15        86.96       115.69 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      101.62       110.50        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       18.12        62.47        11.57        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A73Z TCGA-LL-A740 
       10.62        24.95        32.75        17.06         7.46        14.50 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       22.39         2.10        40.08        34.92        28.87        24.72 
TCGA-OL-A66J TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA15 
       65.62        19.73         0.26        21.07        17.39        17.26 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        15.35        16.04       108.07 

$subtype3
TCGA-5L-AAT0 TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SQ TCGA-A2-A04N 
       48.56         9.96        43.43        47.24        18.21       143.15 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CT TCGA-A2-A0CU 
      121.94        63.12        92.48        88.60        75.25         5.19 
TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      101.72        80.28        74.40        35.05        34.29        31.82 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 
       24.72        63.29        44.28        20.52        17.46        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YL TCGA-A2-A0YT 
       32.55        25.28        50.47        21.67        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A4RW TCGA-A2-A4S2 TCGA-A7-A0CD 
       23.47        60.72        52.47         7.30        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A26E TCGA-A7-A26H 
       34.29        35.47        33.11        29.79        31.36        23.80 
TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       20.61        10.59        14.70        11.97        14.93        13.74 
TCGA-A7-A56D TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06Y 
       14.73        11.05        10.42        13.02         1.02        26.01 
TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A084 
       17.03        19.99        18.97        18.97         7.99        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
       36.95         0.99        19.96        33.01       112.08        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A0A2 TCGA-A8-A0A4 
        1.02        50.04        33.07         1.02        19.04        13.02 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A3EH TCGA-AC-A3TN TCGA-AC-A3YJ 
       27.02        17.03        99.35         6.48        14.99        24.79 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
       19.33        14.96        17.42         1.68         8.22         1.32 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN 
        0.23         0.33         6.44         5.65         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT 
        6.90         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03T TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
        5.33        80.28        47.87        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 
       50.70        72.00        26.24        50.24        62.04        99.25 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KP 
      106.78        98.27        65.56        41.62        40.57        82.62 
TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A24K TCGA-AR-A24L 
       32.91         5.26       107.24       134.14        50.89        94.22 
TCGA-AR-A2LK TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0IC TCGA-B6-A0IN TCGA-B6-A0IO 
       54.21        73.35       281.29        50.70        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0WT 
      129.07        68.45        78.02       263.28       162.05       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A1KN TCGA-B6-A408 
       79.63        18.35       206.86       129.70       139.17        68.12 
TCGA-BH-A0AU TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BS TCGA-BH-A0C1 
       62.93        37.22        32.02        18.21        53.95        44.02 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       38.01        13.91         3.22        15.68        14.30        44.81 
TCGA-BH-A0GZ TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HQ TCGA-BH-A0HW 
       10.78         5.85         2.37        16.96        36.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18J TCGA-BH-A18P 
       27.25        23.93        42.35        44.81        20.12        30.28 
TCGA-BH-A18S TCGA-BH-A1F5 TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A42T TCGA-BH-A5J0 
       66.05        89.16       122.89        55.00        10.52        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12Y TCGA-C8-A26Z TCGA-C8-A273 
        9.63         9.70        11.77        48.53         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A9FZ TCGA-D8-A145 TCGA-D8-A1JN TCGA-D8-A1X8 TCGA-D8-A1X9 
        9.53        19.46        13.48        20.38        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       12.39        14.73        17.69        14.24        17.42        13.45 
TCGA-D8-A27K TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-D8-A73X 
       48.03        12.26        33.37        18.51        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A10F TCGA-E2-A152 TCGA-E2-A155 
       43.00        83.54        34.42        28.87        69.96        21.04 
TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       23.87        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B4 TCGA-E2-A2P6 TCGA-E2-A56Z 
       20.58        56.94        14.07        33.01        34.55         8.28 
TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1R3 
       30.61        39.72        34.29        32.88        36.82         2.56 
TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A295 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
        1.12        34.45        12.33        23.90        23.84        26.70 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1OX TCGA-EW-A1P3 TCGA-EW-A3E8 TCGA-EW-A423 
       26.40        27.85        29.95        52.96        34.03        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DM 
       23.51        15.22         7.40        59.57       216.76       106.06 
TCGA-GM-A3NY TCGA-LD-A66U TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A6FP 
       38.20        21.24        29.23        25.05        15.32        22.26 
TCGA-LL-A6FQ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66H 
        2.63        17.49        27.91        31.99        58.62        26.70 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VR TCGA-PE-A5DC 
       41.92        42.77        26.04        17.36        40.11        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA11 
       64.21        86.96         0.16        18.81        18.48        13.84 
TCGA-S3-AA17 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB44 TCGA-Z7-A8R6 
       13.94        66.84        11.41        29.03       107.05 

$subtype4
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN 
       14.37        48.10        14.27        20.88        13.68        39.32 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0SU TCGA-A2-A0SW 
      101.98        36.13        77.19        61.58        54.64        44.88 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0YI TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G4 
       17.13        49.84        49.48        17.36        22.45        19.56 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A7-A0DA TCGA-A7-A13F TCGA-A7-A13G 
       42.44        17.19       105.34        35.67        25.15        23.61 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07B 
       21.73        22.32        53.06        29.03         1.02        43.00 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08I 
       14.01        12.00        10.98        45.07        13.02        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A09E 
       37.05        31.00        43.00        40.01        30.97        49.05 
TCGA-A8-A09K TCGA-A8-A09T TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0AD TCGA-AC-A23C 
       29.98        19.04        14.01        12.00        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AN-A03X TCGA-AN-A049 TCGA-AN-A0AS 
       22.95         5.72         1.48         0.33         0.62         0.33 
TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03U 
        0.33         5.59        61.35        66.77        81.63        58.95 
TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A126 
       29.13        26.04        50.86        76.77        71.80       108.72 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TV 
        0.53        17.79        24.79       130.09        15.62        75.22 
TCGA-AR-A0TX TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AV 
       64.83        96.00        93.90        37.81        41.82        61.28 
TCGA-AR-A1AW TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U 
       86.53       120.33        99.78       112.77        97.84        77.69 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
      105.30        98.76        98.66        89.00        93.30        85.64 
TCGA-AR-A255 TCGA-B6-A0I8 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IM 
       71.05        24.62       275.87       129.57       146.50       127.33 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS 
      212.25       234.28        81.17       102.77       157.41        97.48 
TCGA-B6-A1KI TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B4 
       73.51        20.45        81.44        37.74        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       70.22        84.13        51.58        43.53        21.70        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DG 
       75.48        74.14        76.60        49.94        90.97        23.44 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0EI TCGA-BH-A0H0 
       15.65         2.56        70.88        16.27        24.43        15.16 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18I 
       23.90        20.38         2.50        12.89        50.79        35.93 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV 
       90.84        37.74        67.50       113.82        82.85        12.00 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 
       17.69        31.53        24.62        45.63       144.59        26.14 
TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12X 
       57.83       130.16        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
       12.56         3.16         1.87        12.92         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HO 
       10.92        11.34        11.28        12.03        10.42        12.33 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD 
       13.25        20.58        21.14        14.17        17.49        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JP 
       18.90        12.03        53.00        18.97        20.09        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB 
       12.20        13.32        17.79        16.73        27.58        18.15 
TCGA-D8-A1XD TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.16        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A109 TCGA-E2-A10A 
       16.54        15.52         9.93        12.53        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       37.51        40.11        28.44        44.68        33.17        75.98 
TCGA-E2-A14V TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15K 
       34.26        23.24        19.43        22.82        17.29         9.04 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE 
       11.05        50.79        19.56        51.39        32.35        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        70.36        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       60.99        11.08        60.36        73.64        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LS TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NG 
       75.81        52.73        34.82        22.29        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       18.94         9.86        34.95         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        45.01        40.24        46.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D 
       47.64        32.05        42.25        37.74        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       41.72        40.50         0.69        38.99         7.13        24.56 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72         8.48        18.21        18.90        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 
       28.77        25.94        29.85        40.41        41.13        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW 
       18.48        13.94        10.52        52.73        22.09 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.03     0.16     0.33 
subtype1 subtype2 subtype3 subtype4 
  255.68   282.90   281.29   275.87 
subtype1 subtype2 subtype3 subtype4 
   24.99    32.58    26.04    29.13 
[1] "0.0 - 255.7 (25.0)" "0.0 - 282.9 (32.6)" "0.2 - 281.3 (26.0)"
[4] "0.3 - 275.9 (29.1)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      14       17        0        2       132        69         0
  subtype2      24       21        2        2        45        58         1
  subtype3      16       27        4        1        89        57         1
  subtype4      35       22        1        1        88        65         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         40          7         13        8         0       3
  subtype2         31          3         23        3         1       0
  subtype3         37         11         20        3         0       8
  subtype4         44          7          8        6         0       3
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          14       24       16       35
  STAGE IA         17       21       27       22
  STAGE IB          0        2        4        1
  STAGE II          2        2        1        1
  STAGE IIA       132       45       89       88
  STAGE IIB        69       58       57       65
  STAGE III         0        1        1        0
  STAGE IIIA       40       31       37       44
  STAGE IIIB        7        3       11        7
  STAGE IIIC       13       23       20        8
  STAGE IV          8        3        3        6
  STAGE TIS         0        1        0        0
  STAGE X           3        0        8        3
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  49 215  32  11
  subtype2  72  95  43   3
  subtype3  67 155  36  15
  subtype4  93 154  23  11
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       49       72       67       93
  T2      215       95      155      154
  T3       32       43       36       23
  T4       11        3       15       11
[1] 4 4
[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
  subtype1 165  90  33  16
  subtype2  89  83  17  24
  subtype3 128  86  30  22
  subtype4 127  97  38  13
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      165       89      128      127
  N1       90       83       86       97
  N2       33       17       30       38
  N3       16       24       22       13
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 259   8
  subtype2 160   3
  subtype3 220   4
  subtype4 248   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  259    8
  subtype2  160    3
  subtype3  220    4
  subtype4  248    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      259      160      220      248
  1        8        3        4        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1 303   6
  subtype2 214   0
  subtype3 272   2
  subtype4 277   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  303    6
  subtype2  214    0
  subtype3  272    2
  subtype4  277    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      303      214      272      277
  MALE          6        0        2        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1 127 144
  subtype2  86 104
  subtype3 106 139
  subtype4 112 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127  144
  subtype2   86  104
  subtype3  106  139
  subtype4  112  126
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       127       86      106      112
  YES      144      104      139      126
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           269
  subtype2                          0                            89
  subtype3                          0                           177
  subtype4                          0                           235
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              9                   5
  subtype2                            106                   0
  subtype3                             66                   0
  subtype4                             18                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     5                                4
  subtype2                     4                                3
  subtype3                     0                               10
  subtype4                     0                               11
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  5             10
  subtype2                  3              9
  subtype3                  8             13
  subtype4                  1             15
D9V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  INFILTRATING CARCINOMA NOS              1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         269       89      177      235
  INFILTRATING LOBULAR CARCINOMA          9      106       66       18
  MEDULLARY CARCINOMA                     5        0        0        1
  METAPLASTIC CARCINOMA                   5        4        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        4        3       10       11
  MUCINOUS CARCINOMA                      5        3        8        1
  OTHER  SPECIFY                         10        9       13       15
[1] 8 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    20                        91
  subtype2                                0    11                        30
  subtype3                                0     9                        43
  subtype4                                1    21                        18
          vv
clus       WHITE
  subtype1   176
  subtype2   169
  subtype3   189
  subtype4   212
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                  20       11        9       21
  BLACK OR AFRICAN AMERICAN              91       30       43       18
  WHITE                                 176      169      189      212
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus         0   1
  subtype1   5 261
  subtype2  11 187
  subtype3  10 212
  subtype4  13 214
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  261
  subtype2   11  187
  subtype3   10  212
  subtype4   13  214
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5       11       10       13
  NOT HISPANIC OR LATINO      261      187      212      214
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 248  46
  subtype2 128  24
  subtype3 219  29
  subtype4 123  17
  subtype5  84  10
  subtype6 114  20
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     294      152      248      140       94      134 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      46       24       29       17       10       20 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK 
      129.14        42.81         9.96        14.27        13.68        31.79 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A0CT 
       63.12       101.98        55.43        36.13        88.60        75.25 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0EO TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T1 
      107.93        34.55        80.28        63.29        44.88        17.13 
TCGA-A2-A0T3 TCGA-A2-A0YC TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV 
       49.84        32.55        21.90        21.67        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3XZ TCGA-A7-A0CJ 
       17.36        42.44        17.19       105.34        50.37        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26J 
       37.45        33.11        25.15        23.61        31.36        20.61 
TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06Y 
       22.32        17.92        10.42        13.02         1.02        26.01 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A084 TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       15.06        37.05         9.99        31.00        33.01       112.08 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       30.97        17.95        41.98         9.99         9.99        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09X 
       49.05        45.07        33.07        25.02        19.04        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A3YJ 
       19.04        13.02        17.03         0.95         5.72        24.79 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A7VB TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
       14.96        11.44         8.22         0.33         0.33         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0XO 
        1.71         7.36         0.16         0.33         7.04        12.33 
TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J3 
        0.33         5.59        80.28        81.63        29.13        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       26.04        22.36        21.53        50.70        50.86        76.77 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KT 
       71.80        99.25        65.56        41.62        82.62        17.79 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
      130.09        15.62        98.33        64.83       107.24        83.87 
TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K 
       37.81        41.82        61.28        86.53       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       94.22        98.76        98.66        89.00        93.30        85.64 
TCGA-AR-A2LK TCGA-B6-A0I8 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IN 
       54.21        24.62       129.57        65.72       146.50        84.59 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0WS TCGA-B6-A0WV 
      165.76        68.45        81.17       263.28        97.48        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       18.35       113.79       206.86        62.93        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BC TCGA-BH-A0BP 
       63.09        37.74        39.16        81.63        32.02        75.48 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DK 
       53.95        45.57        49.94        41.75        90.97        13.91 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 
       70.88        16.27        30.35        10.78        15.16        53.26 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL 
       23.08        41.00        52.96        26.50        20.38         2.37 
TCGA-BH-A0HN TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EO 
       16.96        12.89        27.25        26.66        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F8 
      113.82        82.85        12.00        55.69        31.53        24.62 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A209 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       55.00        45.63       130.16        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A1HE 
       11.77        12.66        48.53        12.56         1.87        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V 
       11.34        11.28        12.03        12.33        12.33        20.25 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A9FZ TCGA-D8-A13Y 
        9.53         0.03         9.50        24.56        19.46        56.81 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD 
       13.25        20.58        14.17        17.49        16.50        18.15 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1XA 
       20.09        20.38        21.01        12.20        18.58        27.58 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       17.16        15.22        14.73        12.99        15.52         9.93 
TCGA-D8-A1Y3 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O 
       14.14        43.00        46.59        40.11        28.44        44.68 
TCGA-E2-A14T TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F 
       75.98        69.96        21.04        23.34        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       18.21        55.63         9.04        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG 
       56.94        14.07        51.39        32.35        77.65        70.36 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
        3.88        22.19        60.99        60.36        73.64        19.66 
TCGA-E2-A1LB TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       75.81        34.29        17.69        36.82        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 
       36.56        35.77        35.24        25.84         9.86        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A226 
        6.12         3.02        11.15        46.65        21.27        34.45 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
       42.25        37.74        38.37        41.72        40.50        38.99 
TCGA-E9-A6HE TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P6 
       27.85        18.21        28.77        25.94        40.41        18.48 
TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA 
        6.15        52.73        25.91        10.16        15.22        16.77 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 
       15.32        14.70         2.63        19.53        12.36        17.49 
TCGA-OL-A5D8 TCGA-OL-A5RZ TCGA-OL-A66H TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA17 
       31.99        22.32        26.70        21.07        13.84        13.94 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SB TCGA-A1-A0SM TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A0CL 
      131.67         8.52         7.96        18.02        78.41        99.12 
TCGA-A2-A0CY TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0ST TCGA-A2-A0SV 
       55.00        33.76        79.76        31.82        99.19        27.12 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A4RW 
       17.52         8.38        19.20        33.93        32.75         7.30 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26I TCGA-A7-A4SD TCGA-A8-A06R TCGA-A8-A06U 
       26.96        21.90        21.73        14.50        17.98        29.03 
TCGA-A8-A075 TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09K 
       17.03         9.99        38.01        43.00        12.00        29.98 
TCGA-A8-A0A7 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
        0.99        33.04        14.66        16.80        14.53        19.33 
TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR 
       12.26         0.03         1.78         9.96         7.46         0.33 
TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 
        0.33         0.33         0.36         0.33         0.33         0.53 
TCGA-AN-A0XN TCGA-AO-A03M TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12D 
        0.33        61.35        32.78        72.00       115.27        64.04 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TT TCGA-AR-A0TY TCGA-AR-A1AO TCGA-AR-A1AU 
        0.53         5.65       109.02        55.86        86.07        94.29 
TCGA-AR-A1AX TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A5QQ TCGA-B6-A0I9 
       86.43        97.84        77.69        99.62        10.59        12.13 
TCGA-B6-A0RS TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
      100.70        39.55        84.13        61.51        74.89        77.95 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0RX TCGA-BH-A18R 
       89.06        45.83        78.28        31.00         5.59        37.55 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 
       51.39        51.16        25.81        72.07        72.07        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A130 
       38.60        57.83        11.93        12.66        12.66         3.16 
TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
       13.51        12.92        10.92        12.95        12.36        12.95 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JC TCGA-D8-A1JF 
       13.02        20.88        13.97        14.17        15.78        12.03 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT TCGA-D8-A1XZ TCGA-D8-A27R TCGA-E2-A108 
       53.00        20.12        16.64        15.32        10.09        27.52 
TCGA-E2-A14P TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15H 
       40.96        32.02        18.51        63.62        25.05        12.92 
TCGA-E2-A1B0 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A574 
       53.62        24.59       106.75        43.04        52.73        38.76 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1OY 
        6.58        46.59        20.12         1.94         0.79        29.85 
TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A6SC TCGA-EW-A6SD 
       39.78        30.08        19.96        55.00        31.30        33.21 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YL 
      216.76        79.10        75.02        72.10        11.84        17.06 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OK-A5Q2 
       14.47        14.79        15.68         7.46        19.59         2.10 
TCGA-OL-A5RW TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A97C TCGA-S3-AA15 TCGA-UL-AAZ6 
       36.36        26.04        14.07         8.91        17.26        17.03 
TCGA-UU-A93S TCGA-WT-AB44 
        3.81        29.03 

$subtype3
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-A2-A04N TCGA-A2-A0CK TCGA-A2-A0CO 
       40.14        11.44        48.56       143.15       136.73       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CZ TCGA-A2-A0EM TCGA-A2-A0EP 
       92.48       107.93         5.19        53.13       101.72       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU 
       74.40        72.00        34.29        61.94        24.72        54.64 
TCGA-A2-A0T4 TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G0 TCGA-A2-A1G6 
       20.52        25.28        19.33        48.46        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW 
       52.47       107.70        18.15        36.23        39.65        56.28 
TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A3IZ 
       21.30        21.14        34.29        29.56        23.80        10.59 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC 
       11.28        14.70        11.97        14.93        13.74        14.66 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E TCGA-AC-A2B8 TCGA-AC-A2BM 
       14.73        10.72        11.05        19.99         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        19.33        32.45        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AN-A0FF 
       23.24        17.42        18.67        20.19         2.30         5.65 
TCGA-AN-A0FS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03T TCGA-AO-A0JI TCGA-AO-A128 
        6.90         0.33         5.33        47.87        50.24       106.78 
TCGA-AO-A1KO TCGA-AQ-A7U7 TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A24T TCGA-AR-A24W 
       14.73        19.20        97.68        98.33       105.27        32.58 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IH 
       39.39        40.54        73.35        33.30        38.96       112.37 
TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0BD 
       78.02       140.48       170.17        85.35        71.15        18.21 
TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DO 
       72.23        49.05        44.02        23.44        29.98        17.26 
TCGA-BH-A0DV TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18M 
       67.86        14.30        46.19        24.95        42.35        72.56 
TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       42.28        49.58       120.62        74.73       122.89        36.92 
TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       28.14        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A137 TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 
       21.76         9.44         4.11        12.53         8.28         9.67 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1JH 
       33.99        12.95        12.49        13.41        55.50        14.01 
TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
       14.70        25.74        23.90        21.80        19.92        17.69 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.24        17.42        13.45        14.43        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A14Q 
       18.51        21.67        16.18        25.22        34.42        38.24 
TCGA-E2-A14U TCGA-E2-A15C TCGA-E2-A15L TCGA-E2-A1B1 TCGA-E2-A1L6 TCGA-E2-A1LE 
       43.33        22.82        20.58        87.22        54.18        28.90 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A572 TCGA-E9-A1N4 
       26.99        34.55        43.56         8.28        39.72        32.88 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A22A 
       24.82        28.27         2.56        32.09         1.12        39.09 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UP 
       12.33        29.72         9.47        30.44        26.70        26.40 
TCGA-EW-A1PA TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 
       18.90        14.43        34.55        34.03        23.51         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN 
       59.57        83.34        85.15        86.96       115.69       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        62.47        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A50Y TCGA-LL-A6FP 
        7.10        13.28        10.62        24.95        25.05        22.26 
TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5DA TCGA-OL-A5RU 
       14.50        27.91        22.39        36.30        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       34.92        28.87        24.72        65.62        41.92        42.77 
TCGA-OL-A66O TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       17.36        19.73        40.11        47.01        64.21        86.96 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA14 TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 
        0.26        18.48        17.39        11.41        52.96        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

$subtype4
TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI 
       48.36        14.37        43.43        48.10        47.24        20.88 
TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0SY 
       39.32        77.19        98.99        61.58        89.36        44.28 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A1FZ TCGA-A7-A0CH 
       17.46        18.90        20.75        49.48        22.45        35.47 
TCGA-A8-A07J TCGA-A8-A08A TCGA-A8-A08Z TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N 
       12.00         0.99        40.01        12.00         1.02         1.02 
TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A3EH TCGA-AC-A4ZE 
       12.00        21.04        22.95        73.91         6.48        29.26 
TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A049 TCGA-AN-A0FD TCGA-AN-A0FN TCGA-AN-A0XL 
        1.68         0.33         0.62         6.44         7.17         5.36 
TCGA-AO-A03N TCGA-AO-A03R TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A126 
       66.77        68.75        53.03        65.10        62.04       108.72 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A0U3 TCGA-AR-A1AK 
       90.58        57.30        32.52         5.26       134.14       103.86 
TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       96.00        93.90       120.33        99.78       118.59         2.76 
TCGA-AR-A24V TCGA-AR-A255 TCGA-B6-A0I5 TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
      105.30        71.05       281.29        18.77       127.33       129.07 
TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0X0 TCGA-B6-A1KI 
      212.25       162.05       102.77       157.41       129.70        73.51 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 
      139.17        68.12       103.63        81.44        40.83        70.22 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BQ TCGA-BH-A0BR 
       37.22        43.53        21.70        61.68        74.14        76.60 
TCGA-BH-A0DE TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0EA TCGA-BH-A0EI 
       77.98        15.65         2.56        38.47        32.58        24.43 
TCGA-BH-A0H3 TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY 
       37.78        23.90         5.85        13.61        36.85        50.79 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P 
       44.81        32.91        35.93        20.12        90.84        30.28 
TCGA-BH-A1EY TCGA-BH-A1FJ TCGA-C8-A138 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JE 
       17.69        63.35         4.08        13.48        21.14        18.90 
TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XY 
       16.73        18.15        55.30        15.85        16.31        16.54 
TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14V TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15D 
       37.51        28.87        34.26        23.24        19.43        17.29 
TCGA-E2-A15J TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1IJ 
       53.92        33.01        37.25        37.41        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IU TCGA-E2-A570 TCGA-E9-A1NH TCGA-E9-A1RA TCGA-E9-A1RC 
       59.18        11.08        30.61        18.94        45.01        40.24 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A249 TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       47.64        32.05         7.13        12.20        39.72         8.48 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-EW-A1PD TCGA-EW-A1PE 
       13.25        16.57        15.68        52.96        13.94        10.52 
TCGA-S3-A6ZF TCGA-Z7-A8R6 
       18.81       107.05 

$subtype5
TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0YF TCGA-A2-A1FX 
       18.21       121.94        25.22        35.05        50.47        60.72 
TCGA-A2-A1G4 TCGA-A2-A4S0 TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A3IY TCGA-A7-A3J0 
       19.56        23.21        38.30        29.79        11.34        10.29 
TCGA-A7-A3RF TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A07L TCGA-A8-A07P 
       13.41        13.02        53.06         1.02        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08I 
        7.99        45.07        36.95        13.02        19.96        12.00 
TCGA-A8-A091 TCGA-A8-A09R TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A8OR TCGA-AN-A041 
       33.01         8.98        27.02        38.04         1.32         0.23 
TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A0JG TCGA-AO-A12B 
        7.00         0.30         0.33        20.32        26.24        98.27 
TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AQ-A54O TCGA-AR-A0TV TCGA-AR-A24R 
       40.57        61.87        24.79        32.91        75.22       112.77 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0RI TCGA-B6-A0WT TCGA-B6-A0X4 TCGA-B6-A0X5 
      275.87        50.70       234.28       188.68        28.27        68.94 
TCGA-B6-A1KC TCGA-BH-A0B8 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E7 
       43.59        51.58        38.01         3.22        15.68        44.81 
TCGA-BH-A0H6 TCGA-BH-A0HO TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18N TCGA-BH-A18S 
       24.56         2.50        51.32        23.93        37.74        66.05 
TCGA-BH-A1F5 TCGA-BH-A1FR TCGA-BH-A204 TCGA-C8-A12X TCGA-C8-A1HL TCGA-D8-A1JI 
       89.16       144.59        83.31        12.66        10.42        18.97 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XC TCGA-D8-A1XV TCGA-D8-A73W TCGA-E2-A106 
       13.32        17.79        12.39        15.16        12.66        83.54 
TCGA-E2-A10A TCGA-E2-A14S TCGA-E2-A156 TCGA-E2-A1BC TCGA-E9-A1N3 TCGA-E9-A1R7 
       40.41        33.17        23.87        16.47        34.82        48.23 
TCGA-E9-A22D TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO 
       41.03        24.56        32.91        23.90        23.84        25.81 
TCGA-EW-A1J1 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A2FW TCGA-GM-A2DM 
       18.90        29.95        41.13        23.11        22.09       106.06 
TCGA-LL-A442 TCGA-PL-A8LX TCGA-S3-AA12 TCGA-V7-A7HQ 
       29.23         0.16        18.87        66.84 

$subtype6
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 
       28.01        19.20        73.84        87.25        24.79        67.33 
TCGA-A2-A0SX TCGA-A2-A0YM TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       50.43        31.73        10.59        91.07        29.98        47.31 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D 
       35.93        50.83        24.39        35.31        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV 
       20.19        24.26        23.74        21.17        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
        9.37         8.75        33.99         9.99         8.98        24.99 
TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A0FJ 
        0.99        73.05        13.71        13.58         1.12         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 
        7.59         0.33         0.33        58.95        52.18        37.48 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N 
       55.33       108.03        48.36        70.39        26.93         2.56 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      140.55        84.10       107.21       125.16       108.36       101.00 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LR 
       99.32        17.23        33.73       104.28        93.83        57.27 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE 
       77.62       143.38        32.58       233.62       140.88       255.68 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A3ZX 
       89.46       282.90        21.47        58.88       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0E0 
        7.07        70.16        18.84        59.84        51.68         4.41 
TCGA-BH-A0E6 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1F6 
        9.63        23.05         4.90        55.63         7.36        97.48 
TCGA-BH-A1FC TCGA-BH-A5IZ TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B 
      114.15        18.64        12.66        12.59         0.16        14.43 
TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F 
       19.20        20.09        14.50        16.41        43.04        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       13.05        13.48        47.15        38.60        31.96        69.34 
TCGA-E2-A158 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LI 
       14.79        76.57        28.50        33.70        50.07       102.61 
TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A244 
        8.75        34.92        34.16        41.62        40.73         0.69 
TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A3U0 
       30.18        22.82        29.82         7.86        19.99        17.49 
TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A441 
       24.99       109.87        70.85        69.30         2.60        32.75 
TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ 
       16.08        58.52        20.38        23.47        28.21         9.93 
TCGA-S3-AA0Z TCGA-S3-AA10 
       20.68        19.27 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.03     0.26     0.33     0.16     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  263.28   216.76   170.17   281.29   275.87   282.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  26.270   21.815   25.510   36.390   26.630   30.955 
[1] "0.0 - 263.3 (26.3)" "0.0 - 216.8 (21.8)" "0.3 - 170.2 (25.5)"
[4] "0.3 - 281.3 (36.4)" "0.2 - 275.9 (26.6)" "0.2 - 282.9 (31.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      18       23        2        2        96        67         1
  subtype2      12        9        1        2        56        33         0
  subtype3      16       29        2        1        62        67         1
  subtype4      26        8        1        0        44        32         0
  subtype5       9        6        1        0        32        23         0
  subtype6       8       12        0        1        64        27         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         48          8         17        7         1       8
  subtype2         23          3          9        6         0       0
  subtype3         40          3         24        1         0       2
  subtype4         11          6          9        3         0       1
  subtype5         18          6          1        1         0       1
  subtype6         12          2          4        2         0       2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          18       12       16       26        9        8
  STAGE IA         23        9       29        8        6       12
  STAGE IB          2        1        2        1        1        0
  STAGE II          2        2        1        0        0        1
  STAGE IIA        96       56       62       44       32       64
  STAGE IIB        67       33       67       32       23       27
  STAGE III         1        0        1        0        0        0
  STAGE IIIA       48       23       40       11       18       12
  STAGE IIIB        8        3        3        6        6        2
  STAGE IIIC       17        9       24        9        1        4
  STAGE IV          7        6        1        3        1        2
  STAGE TIS         1        0        0        0        0        0
  STAGE X           8        0        2        1        1        2
[1] 13  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  70 182  34  12
  subtype2  40  95  15   5
  subtype3  66 128  49   4
  subtype4  51  69  13   8
  subtype5  26  53  12   7
  subtype6  28  92  11   4
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       70       40       66       51       26       28
  T2      182       95      128       69       53       92
  T3       34       15       49       13       12       11
  T4       12        5        4        8        7        4
[1] 4 6
[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
  subtype1 121 106  40  22
  subtype2  74  44  23  11
  subtype3 111  85  23  26
  subtype4  73  47  10  11
  subtype5  43  40  12   1
  subtype6  87  34  10   4
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0      121       74      111       73       43       87
  N1      106       44       85       47       40       34
  N2       40       23       23       10       12       10
  N3       22       11       26       11        1        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1 251   8
  subtype2 126   6
  subtype3 186   1
  subtype4 123   3
  subtype5  85   1
  subtype6 116   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  251    8
  subtype2  126    6
  subtype3  186    1
  subtype4  123    3
  subtype5   85    1
  subtype6  116    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      251      126      186      123       85      116
  1        8        6        1        3        1        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1 296   4
  subtype2 152   3
  subtype3 248   0
  subtype4 139   2
  subtype5  95   3
  subtype6 136   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  296    4
  subtype2  152    3
  subtype3  248    0
  subtype4  139    2
  subtype5   95    3
  subtype6  136    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      296      152      248      139       95      136
  MALE          4        3        0        2        3        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1 112 152
  subtype2  60  75
  subtype3 106 125
  subtype4  60  51
  subtype5  41  42
  subtype6  52  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  112  152
  subtype2   60   75
  subtype3  106  125
  subtype4   60   51
  subtype5   41   42
  subtype6   52   68
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO       112       60      106       60       41       52
  YES      152       75      125       51       42       68
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           252
  subtype2                          0                           131
  subtype3                          0                           100
  subtype4                          0                            99
  subtype5                          0                            70
  subtype6                          1                           118
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             22                   1
  subtype2                             11                   0
  subtype3                            134                   0
  subtype4                             28                   0
  subtype5                              2                   0
  subtype6                              2                   5
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               10
  subtype2                     6                                1
  subtype3                     1                                3
  subtype4                     0                                9
  subtype5                     0                                3
  subtype6                     2                                2
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  1             14
  subtype2                  0              6
  subtype3                  3              7
  subtype4                  0              5
  subtype5                 13             10
  subtype6                  0              5
D10V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         252      131      100       99       70
  INFILTRATING LOBULAR CARCINOMA         22       11      134       28        2
  MEDULLARY CARCINOMA                     1        0        0        0        0
  METAPLASTIC CARCINOMA                   0        6        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        1        3        9        3
  MUCINOUS CARCINOMA                      1        0        3        0       13
  OTHER  SPECIFY                         14        6        7        5       10
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              1
  INFILTRATING DUCTAL CARCINOMA         118
  INFILTRATING LOBULAR CARCINOMA          2
  MEDULLARY CARCINOMA                     5
  METAPLASTIC CARCINOMA                   2
  MIXED HISTOLOGY (PLEASE SPECIFY)        2
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          5
[1] 8 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    22                        44
  subtype2                                0    13                        27
  subtype3                                0    12                        39
  subtype4                                0     5                         8
  subtype5                                0     4                        10
  subtype6                                0     5                        54
          vv
clus       WHITE
  subtype1   197
  subtype2   102
  subtype3   194
  subtype4   119
  subtype5    64
  subtype6    70
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                  22       13       12        5        4
  BLACK OR AFRICAN AMERICAN              44       27       39        8       10
  WHITE                                 197      102      194      119       64
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   5
  BLACK OR AFRICAN AMERICAN              54
  WHITE                                  70
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus         0   1
  subtype1   7 230
  subtype2   6 127
  subtype3  10 224
  subtype4   8 110
  subtype5   5  65
  subtype6   3 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  230
  subtype2    6  127
  subtype3   10  224
  subtype4    8  110
  subtype5    5   65
  subtype6    3  118
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            7        6       10        8        5        3
  NOT HISPANIC OR LATINO      230      127      224      110       65      118
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 152  29
  subtype2 120  18
  subtype3  94   7
  subtype4  96  15
  subtype5 115  17
subtype1 subtype2 subtype3 subtype4 subtype5 
     181      138      101      111      132 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       18        7       15       17 
$subtype1
TCGA-3C-AAAU TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0T3 TCGA-A2-A1FW 
      129.14        39.32        77.19        61.58        49.84        17.36 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A7-A13F TCGA-A7-A13G 
       22.45        20.25        19.56        42.44        25.15        23.61 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A3EH 
       10.29        13.41         0.95        22.95         5.72         6.48 
TCGA-AC-A7VB TCGA-AO-A03V TCGA-AO-A12A TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KS 
        8.22        29.13        90.58        40.57        82.62         0.53 
TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AR-A0TY TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AT 
       17.79        15.62        55.86       103.86        93.90        41.82 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R 
       61.28       160.90        94.22       120.33        99.78       112.77 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
      105.30        98.76        98.66        89.00        93.30        71.05 
TCGA-B6-A0RH TCGA-B6-A1KN TCGA-BH-A0AU TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BR 
      212.25       139.17        62.93        84.13        75.48        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0H5 TCGA-BH-A0HA 
       53.95        45.57        45.83        23.44        53.26        52.96 
TCGA-BH-A0HN TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S 
       16.96        35.93        90.84        26.66        37.74        66.05 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 
       67.50       113.82        12.00        49.58        17.69        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 
       24.62        55.00        45.63       144.59        26.14        83.31 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.87         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A27A 
       12.03        10.42        12.33        12.95        12.33        24.56 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC 
       56.81        13.25        20.58        14.17        17.49        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JP TCGA-D8-A1JS 
       18.15        18.90        18.97        20.09        21.01        12.20 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        17.79        16.73        27.58        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV 
       15.22        55.30        15.85        16.31        12.99        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A10A TCGA-E2-A14O 
       16.54        15.52         9.93        12.53        40.41        44.68 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15C TCGA-E2-A15G 
       75.98        32.02        69.96        19.43        22.82        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T 
       12.92        55.63         9.04        50.79        56.94        51.39 
TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.35        77.65        70.36         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E9-A1N3 TCGA-E9-A1N6 
       11.08        73.64        19.66        75.81        34.82        22.29 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R2 TCGA-E9-A1R4 
       35.77        35.24        25.84        18.94        34.95         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RE 
        3.02        11.15        48.23        45.01        40.24        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B 
        6.58        21.27        47.64        42.25        37.74        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       41.03        41.72        40.50        38.99         7.13        24.56 
TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
        8.48        18.90        16.57        15.68        28.77        25.94 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P6 TCGA-EW-A2FS TCGA-EW-A2FW 
       29.85        40.41        41.13        18.48        52.73        22.09 
TCGA-OL-A5RZ 
       22.32 

$subtype2
TCGA-3C-AALI TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT 
      131.67        87.25        99.12        19.20        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0DA 
       29.98        47.31        50.83        24.39        26.96        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A7-A6VV 
       31.73        20.19        21.73        14.50        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW 
        9.37         8.75        73.05        16.57        13.71        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A0AT TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
        0.03         1.12         0.33        48.36        61.87        70.39 
TCGA-AR-A0TS TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
       84.10       125.16       108.36       101.00        99.32        17.23 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 
       86.53        33.73       104.28        97.84        77.69        99.62 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A3ZX 
       85.64        93.83        10.59        77.62       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
        7.07        70.16        18.84        61.51        74.89        77.95 
TCGA-BH-A0DL TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FN 
       78.28        37.55        51.16        25.81        97.48        72.07 
TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 
      130.16        18.64        11.93        12.66        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A143 
       12.92         0.16         9.50        14.43        13.02        14.17 
TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ 
       19.20        53.00        20.12        20.09        14.50        16.41 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27M 
       16.64        43.04        15.32        14.14        16.04        13.48 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       47.15        40.96        38.60        31.96        69.34        63.62 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II 
       25.05        11.05        76.57        53.62        28.50        33.70 
TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS 
       60.36        24.59       106.75       102.61         8.75        52.73 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
       34.92        38.76        17.69        34.16        36.20        41.62 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-EW-A1IZ 
       46.59        40.73         0.69         1.94        30.18        18.21 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3U0 
       22.82        29.82        30.08        19.99         6.15        17.49 
TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A441 
       24.99       109.87        70.85        69.30         2.60        32.75 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A5S0 
       14.47        14.79        16.08        15.68        36.36        20.38 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
       23.47        14.07        28.21         9.93        20.68        19.27 

$subtype3
TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A2-A1FV 
       42.81        40.14        48.56        48.36         9.96        23.47 
TCGA-A2-A1FX TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
       60.72         7.30        21.30        23.21        21.14        21.90 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        13.74        14.66        17.92        14.73 
TCGA-A7-A5ZX TCGA-AC-A4ZE TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       11.05        29.26        19.33        14.96        11.44        17.42 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AQ-A54O TCGA-AR-A5QM TCGA-AR-A5QN 
        1.68        20.19         1.32        32.91        73.35        33.30 
TCGA-AR-A5QP TCGA-B6-A408 TCGA-BH-A0DO TCGA-BH-A0HL TCGA-BH-A42T TCGA-BH-A42U 
       38.96        68.12        17.26         2.37        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A8FY TCGA-BH-AB28 TCGA-C8-A9FZ TCGA-D8-A3Z5 
       20.88        23.51         9.70         9.44        19.46        33.37 
TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A15F TCGA-E2-A56Z TCGA-E2-A570 
       21.67        38.24        33.17        21.63         8.28        30.61 
TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       39.72        34.29        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6SA TCGA-GM-A3XG TCGA-GM-A4E0 
       27.85        34.03        23.51        16.77        43.73        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A442 
       13.55        18.12        62.47        21.24        13.28        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
       25.05        17.06        15.32        14.70        22.26         2.63 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       58.62        40.08        34.92        28.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DC TCGA-PE-A5DD 
       65.62        41.92        42.77        26.04        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA17 TCGA-UL-AAZ6 
       86.96         0.16        13.84        18.87        13.94        17.03 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35       108.07       107.05 

$subtype4
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A2-A04W 
       11.44         8.52        14.37        48.10        20.88       101.98 
TCGA-A2-A0CV TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A1G6 TCGA-A7-A26E TCGA-A7-A26G 
       98.99       118.45        72.00        16.47        31.36        23.74 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A4SE TCGA-A7-A5ZW TCGA-AC-A23G TCGA-AC-A2B8 
       20.61        11.34        21.17        10.72        73.91         1.48 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A5EH TCGA-AC-A5EI 
       90.71        60.92        14.66        23.24        16.80        14.53 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OS TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       18.67        12.26         2.30        14.73        32.52        19.20 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A24O TCGA-AR-A24P 
       97.68        96.00        86.07        94.29       118.59         2.76 
TCGA-B6-A0IH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 
      112.37        97.48        73.51        63.09        81.44        70.22 
TCGA-BH-A0BQ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DT 
       74.14        89.06        90.97        77.98        29.98        38.47 
TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A18F TCGA-BH-A18M 
       70.88        46.19        24.43        37.78        32.91        72.56 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE 
       91.99        42.28        55.69        31.53       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A6R9 
       36.92        72.07        28.14        57.83        10.65         5.26 
TCGA-BH-A8G0 TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB 
       21.76        13.41        20.88        13.48        21.14        55.50 
TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1XB TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A14U 
       14.01        14.70        18.15        16.18        25.22        43.33 
TCGA-E2-A153 TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC 
       23.24        17.29        20.71        87.22        33.01        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1L6 TCGA-E2-A3DX 
       37.25        33.73        28.44        59.18        54.18        43.56 
TCGA-E9-A1QZ TCGA-E9-A227 TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1IX 
       24.82        32.05        30.44         0.79        12.20        39.72 
TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PD TCGA-EW-A1PG TCGA-EW-A2FR TCGA-GM-A3XN 
       13.25        39.78        13.94        34.55        55.00        66.38 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A740 TCGA-OL-A97C TCGA-PL-A8LY TCGA-S3-AA14 
       10.62        24.95        14.50         8.91         0.26        17.39 
TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A89A 
       17.26        11.41        16.04 

$subtype5
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A25A TCGA-A2-A25D 
      136.73       114.81       107.93       107.93       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       36.23        39.65        32.75        56.28        35.93        50.37 
TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 
       33.11        29.56        23.80        22.32        10.59        11.28 
TCGA-A7-A6VX TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FK TCGA-AC-A2FM 
       10.42        99.35        40.57        86.66        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       74.14        33.04        19.33        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 
       22.19        24.13        25.05        14.99        19.79        15.48 
TCGA-AC-A3YJ TCGA-AR-A1AM TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       24.79        98.33        20.25        86.53        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-B6-A2IU 
       63.62        38.17        39.39        40.54        57.27       170.17 
TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 TCGA-BH-A0E2 TCGA-BH-A0W7 
       85.35       103.63        71.15        81.63        14.30        44.81 
TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A130 
       38.60         6.44        20.12         9.63        18.87         3.16 
TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        4.11        20.25        12.53        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        9.67         9.53         0.03        33.99        12.95        12.49 
TCGA-D8-A1X9 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       23.90        17.42        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       16.41         4.80         1.61        10.09        13.08        12.26 
TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-E2-A15P TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.51        12.66        19.56        28.90        26.99        34.55 
TCGA-E9-A1R0 TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS 
       28.27         1.12        34.45        39.09        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-EW-A1PA TCGA-EW-A2FV TCGA-EW-A6S9 TCGA-EW-A6SC 
        9.47        32.91        18.90        25.91        15.22        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21         7.40        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-JL-A3YW TCGA-JL-A3YX 
      101.62        85.35       110.50        38.20        11.84        11.57 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A6VQ 
       13.22         7.10         7.46        19.53        12.36        19.73 
TCGA-OL-A6VR TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UU-A93S TCGA-V7-A7HQ 
       40.11        18.81        18.48        21.07         3.81        66.84 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.53     0.03     0.16     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  212.25   131.67   109.28   120.62   216.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
   26.14    29.90    23.51    30.44    25.48 
[1] "0.5 - 212.2 (26.1)" "0.0 - 131.7 (29.9)" "0.2 - 109.3 (23.5)"
[4] "0.3 - 120.6 (30.4)" "0.0 - 216.8 (25.5)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      20       17        1        1        63        41         0
  subtype2      10        7        0        1        65        28         0
  subtype3       5       12        3        2        25        24         0
  subtype4      15        8        1        0        31        30         0
  subtype5      12        8        0        1        35        39         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         26          4          6        1       1
  subtype2         20          3          3        1       0
  subtype3         14          1         13        3       0
  subtype4         14          2          7        1       1
  subtype5         18          3         13        2       0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          20       10        5       15       12
  STAGE IA         17        7       12        8        8
  STAGE IB          1        0        3        1        0
  STAGE II          1        1        2        0        1
  STAGE IIA        63       65       25       31       35
  STAGE IIB        41       28       24       30       39
  STAGE III         0        0        0        0        2
  STAGE IIIA       26       20       14       14       18
  STAGE IIIB        4        3        1        2        3
  STAGE IIIC        6        3       13        7       13
  STAGE IV          1        1        3        1        2
  STAGE X           1        0        0        1        0
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  60 101  14   6
  subtype2  28  97  10   5
  subtype3  23  56  21   2
  subtype4  42  53  14   2
  subtype5  32  71  26   4
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       60       28       23       42       32
  T2      101       97       56       53       71
  T3       14       10       21       14       26
  T4        6        5        2        2        4
[1] 4 5
[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
  subtype1 85 67 19  7
  subtype2 82 36 19  3
  subtype3 45 34  7 13
  subtype4 48 45 10  7
  subtype5 58 47 12 15
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       85       82       45       48       58
  N1       67       36       34       45       47
  N2       19       19        7       10       12
  N3        7        3       13        7       15
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus         0   1
  subtype1 158   1
  subtype2 112   1
  subtype3  56   3
  subtype4  84   1
  subtype5 105   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  158    1
  subtype2  112    1
  subtype3   56    3
  subtype4   84    1
  subtype5  105    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      158      112       56       84      105
  1        1        1        3        1        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus         0   1
  subtype1 178   4
  subtype2 139   1
  subtype3  99   3
  subtype4 110   1
  subtype5 133   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  178    4
  subtype2  139    1
  subtype3   99    3
  subtype4  110    1
  subtype5  133    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      178      139       99      110      133
  MALE          4        1        3        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
          cls
clus        0  1
  subtype1 82 80
  subtype2 53 74
  subtype3 41 54
  subtype4 40 49
  subtype5 59 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82   80
  subtype2   53   74
  subtype3   41   54
  subtype4   40   49
  subtype5   59   70
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        82       53       41       40       59
  YES       80       74       54       49       70
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           146
  subtype2                          1                           123
  subtype3                          0                            41
  subtype4                          0                            63
  subtype5                          0                            64
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             13                   0
  subtype2                              3                   5
  subtype3                             52                   0
  subtype4                             34                   0
  subtype5                             58                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                8
  subtype2                     4                                2
  subtype3                     0                                2
  subtype4                     3                                2
  subtype5                     2                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  6              9
  subtype2                  0              2
  subtype3                  4              3
  subtype4                  1              8
  subtype5                  4              4
D11V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         146      123       41       63       64
  INFILTRATING LOBULAR CARCINOMA         13        3       52       34       58
  MEDULLARY CARCINOMA                     0        5        0        0        0
  METAPLASTIC CARCINOMA                   0        4        0        3        2
  MIXED HISTOLOGY (PLEASE SPECIFY)        8        2        2        2        1
  MUCINOUS CARCINOMA                      6        0        4        1        4
  OTHER  SPECIFY                          9        2        3        8        4
[1] 8 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                        11   151
  subtype2    10                        54    74
  subtype3     1                        39    60
  subtype4     4                        14    92
  subtype5    16                        27    89
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20       10        1        4       16
  BLACK OR AFRICAN AMERICAN       11       54       39       14       27
  WHITE                          151       74       60       92       89
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
          cls
clus         0   1
  subtype1   8 167
  subtype2   3 130
  subtype3   4  90
  subtype4   7  97
  subtype5   7 124
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  167
  subtype2    3  130
  subtype3    4   90
  subtype4    7   97
  subtype5    7  124
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            8        3        4        7        7
  NOT HISPANIC OR LATINO      167      130       90       97      124
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 258  46
  subtype2 224  25
  subtype3  95  15
subtype1 subtype2 subtype3 
     304      249      110 
subtype1 subtype2 subtype3 
      46       25       15 
$subtype1
TCGA-3C-AAAU TCGA-5T-A9QA TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0T3 TCGA-A2-A1FV 
      129.14         9.96        87.25        99.12        49.84        23.47 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       17.36        19.20        19.56        42.44        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S0 
       29.98        32.75        47.31        35.93        50.83        23.21 
TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       26.96        35.67        31.73        20.19        25.15        23.61 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SF 
       23.74        21.73        10.29        13.41        14.50        17.92 
TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A23C TCGA-AC-A23H 
       12.10        10.29         9.37         8.75         0.95         5.72 
TCGA-AC-A2BK TCGA-AC-A3YJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A7VB TCGA-AC-A8OR 
       73.05        24.79        13.71        13.58         8.22         1.32 
TCGA-AN-A0AT TCGA-AO-A03V TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ 
        0.33        29.13        48.36        40.57        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A1AH 
       70.39         0.53        15.62        84.10        55.86       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
      108.36       101.00       103.86        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY 
       17.23        41.82        94.29        61.28        86.53        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
      160.90        94.22       118.59       104.28       112.77        97.84 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       77.69        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A1KF 
       85.64        71.05        93.83        57.27        77.62       101.52 
TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AU 
      139.17        37.87         7.07        70.16        18.84        62.93 
TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS 
       84.13        61.51        74.89        75.48        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DL 
       45.57        77.95        89.06        90.97        45.83        78.28 
TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A18F TCGA-BH-A18K 
       53.26        52.96         2.37        16.96        32.91        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN 
       26.66        37.74        37.55        66.05        51.16        67.50 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 
      113.82        12.00        55.69        49.58        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       97.48        24.62        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A8FY 
       72.07        26.14        83.31       130.16        18.64         9.70 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.93        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       48.53         3.16        13.51         1.87        12.59        12.92 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A278 TCGA-C8-A27A 
       10.42        12.33        12.95        12.33         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A147 
       14.43        19.46        56.81        13.25        14.17        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ 
       14.17        17.49        15.78        53.00        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.12        20.09        12.20        18.58        17.79        16.73 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XQ 
       27.58        12.39        17.16        15.22        14.50        16.41 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       15.85        16.64        15.16        43.04        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27V TCGA-E2-A10A 
        9.93        14.14        17.42        16.04        12.53        40.41 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W 
       47.15        40.96        38.60        33.17        75.98        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15E 
       31.96        69.34        63.62        69.96        25.05        20.71 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R 
       12.92        55.63         9.04        11.05        50.79        56.94 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE 
       51.39        76.57        53.62        32.35        28.50        77.65 
TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       70.36        33.70         3.88        60.36        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A573 
       75.81       106.75       102.61         8.75        52.73        34.92 
TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
       38.76        34.82        22.29        34.16        36.20        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       35.77        35.24        18.94        34.95         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       11.15        48.23        45.01        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       46.59        42.25        38.37        41.03        40.73        40.50 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
        0.69        38.99        24.56        32.91        30.18        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 
       25.81        26.40        18.21        18.90        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        22.82        29.85        40.41        41.13 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FS 
       29.82        18.48        30.08        19.99         6.15        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD 
       25.91        22.09        17.49        16.77        24.99        33.21 
TCGA-GI-A2C9 TCGA-GM-A2DM TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A442 TCGA-LL-A5YO 
      109.87       106.06        69.30         2.60        29.23        14.47 
TCGA-LL-A5YP TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       14.79        15.68        36.36        22.32        20.38        23.47 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
       14.07        28.21         0.16         9.93        20.68        19.27 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.87        13.94        17.03         3.81 

$subtype2
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0EP TCGA-A2-A1FX 
      136.73       114.81       107.93       107.93       118.45        60.72 
TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ 
      107.70        18.15        36.23        39.65        56.28        50.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0DB 
        7.30        24.39        21.30        21.14        21.90        33.11 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       29.56        31.36        23.80        20.61        22.32        10.59 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SE 
       11.28        14.70        14.93        13.74        14.66        21.17 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-AC-A23G TCGA-AC-A2BM 
       14.73        10.72        11.05        10.42        73.91        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        86.66        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       15.48        23.24        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       14.96        11.44        17.42        12.26         1.68         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM 
       20.19         1.12         2.30        32.91        19.20        98.33 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        73.35        33.30        38.96        10.59 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 
      170.17        85.35        68.12       103.63        71.15        81.63 
TCGA-BH-A0DO TCGA-BH-A0E2 TCGA-BH-A203 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       17.26        14.30        38.60        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28        20.88        23.51         9.63         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W 
       18.87        21.76         9.44         4.11        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A1X9 
       33.99        12.95        13.02        12.49        13.41        23.90 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        10.09        13.08        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A14O 
       18.51        21.67        16.18        12.66        25.22        44.68 
TCGA-E2-A14U TCGA-E2-A15F TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       43.33        21.63        28.90        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1R0 
        8.28        30.61        39.72        34.29        17.69        28.27 
TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.12        34.45        39.09        12.33        29.72         9.47 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1PA TCGA-EW-A2FR 
       30.44        26.70         0.79        27.85        18.90        55.00 
TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.03        23.51        15.22        31.30         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       85.15        86.96       115.69       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        32.75        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z 
       15.32        14.70        22.26         2.63        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        19.53        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       28.87        24.72        26.70        41.92        42.77        26.04 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 
        0.26        18.81        18.48        21.07        13.84        17.39 
TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       17.26        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

$subtype3
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W 
        8.52        14.37        48.10        20.88        39.32       101.98 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES TCGA-A2-A1FZ TCGA-A2-A1G0 
       77.19        98.99        61.58        72.00        22.45        20.25 
TCGA-A2-A1G6 TCGA-A7-A3IY TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG 
       16.47        11.34        22.95         1.48        90.71        60.92 
TCGA-AC-A6IV TCGA-AO-A12A TCGA-AO-A1KO TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AR-A1AL 
       18.67        90.58        14.73        17.79        32.52        97.68 
TCGA-AR-A1AN TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24V TCGA-B6-A0IH 
       96.00       120.33        99.78         2.76       105.30       112.37 
TCGA-B6-A0RH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 
      212.25        97.48        73.51        63.09        81.44        70.22 
TCGA-BH-A0BQ TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DX 
       74.14        77.98        23.44        29.98        38.47        70.88 
TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18M 
       46.19        24.43        37.78        44.81        35.93        72.56 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE 
       91.99        42.28        17.69        31.53       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A208 TCGA-C8-A12N TCGA-C8-A138 TCGA-D8-A13Z 
       36.92        28.14        57.83        11.77         4.08        20.88 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        13.48        21.14        55.50        18.15        18.90 
TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XB TCGA-D8-A1XO TCGA-D8-A1XS 
       14.01        21.01        14.70        18.15        55.30        16.31 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-E2-A14Q TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15C 
       12.99        16.54        38.24        23.24        19.43        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC 
       17.29        18.21        19.56        87.22        33.01        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       37.25        33.73        28.44        59.18        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1RC 
       11.08        54.18        73.64        25.84        24.82        40.24 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A249 
       47.64        32.05        37.74        41.72         1.94         7.13 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PD 
       12.20        39.72         8.48        13.25        39.78        13.94 
TCGA-EW-A1PG TCGA-OL-A66J 
       34.55        65.62 

subtype1 subtype2 subtype3 
    0.16     0.03     1.48 
subtype1 subtype2 subtype3 
  160.90   216.76   212.25 
subtype1 subtype2 subtype3 
   29.18    22.26    33.37 
[1] "0.2 - 160.9 (29.2)" "0.0 - 216.8 (22.3)" "1.5 - 212.2 (33.4)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      27       22        1        3       124        68         0
  subtype2      16       20        4        2        62        67         2
  subtype3      19       10        0        0        33        27         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         44          7          7        3       1
  subtype2         37          5         31        3       0
  subtype3         11          1          4        2       1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          27       16       19
  STAGE IA         22       20       10
  STAGE IB          1        4        0
  STAGE II          3        2        0
  STAGE IIA       124       62       33
  STAGE IIB        68       67       27
  STAGE III         0        2        0
  STAGE IIIA       44       37       11
  STAGE IIIB        7        5        1
  STAGE IIIC        7       31        4
  STAGE IV          3        3        2
  STAGE X           1        0        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  78 193  26  11
  subtype2  61 130  53   5
  subtype3  46  55   6   3
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       78       61       46
  T2      193      130       55
  T3       26       53        6
  T4       11        5        3
[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
  subtype1 160  99  37   8
  subtype2 107  85  22  32
  subtype3  51  45   8   5
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      160      107       51
  N1       99       85       45
  N2       37       22        8
  N3        8       32        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
          cls
clus         0   1
  subtype1 258   3
  subtype2 167   3
  subtype3  90   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  258    3
  subtype2  167    3
  subtype3   90    2
   clus
vv  subtype1 subtype2 subtype3
  0      258      167       90
  1        3        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"
D12V7, binary
          cls
clus         0   1
  subtype1 304   5
  subtype2 247   2
  subtype3 108   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  304    5
  subtype2  247    2
  subtype3  108    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      304      247      108
  MALE          5        2        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"
D12V8, binary
          cls
clus         0   1
  subtype1 131 146
  subtype2 104 131
  subtype3  40  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  131  146
  subtype2  104  131
  subtype3   40   50
     clus
vv    subtype1 subtype2 subtype3
  NO       131      104       40
  YES      146      131       50
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           253
  subtype2                          0                           103
  subtype3                          0                            81
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             16                   5
  subtype2                            126                   0
  subtype3                             18                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     2                                9
  subtype2                     7                                2
  subtype3                     0                                4
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  9             14
  subtype2                  5              6
  subtype3                  1              6
D12V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         253      103       81
  INFILTRATING LOBULAR CARCINOMA         16      126       18
  MEDULLARY CARCINOMA                     5        0        0
  METAPLASTIC CARCINOMA                   2        7        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        9        2        4
  MUCINOUS CARCINOMA                      9        5        1
  OTHER  SPECIFY                         14        6        6
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    27                        67   213
  subtype2    18                        72   156
  subtype3     6                         6    97
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           27       18        6
  BLACK OR AFRICAN AMERICAN       67       72        6
  WHITE                          213      156       97
[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"
D12V12, binary
          cls
clus         0   1
  subtype1  14 280
  subtype2   9 230
  subtype3   6  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  280
  subtype2    9  230
  subtype3    6   98
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        9        6
  NOT HISPANIC OR LATINO      280      230       98
[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"
