[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/22506573/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.mergedcluster.txt"

nPatients in clinical file=1097, in cluster file=1098, common to both=1097
[1]   12 1097
[1] "MRNA_CNMF"
[1] 3
  1   2   3 
234 118 174 
  1   2   3 
234 118 174 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3 
162 272  92 
  1   2   3 
162 272  92 
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
330 131 295 294  29 
  1   2   3   4   5 
330 131 295 294  29 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
224 184 145 141  88 
  1   2   3   4   5 
224 184 145 141  88 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5   6   7 
199 239  30 208 133  67  10 
  1   2   3   4   5   6   7 
199 239  30 208 133  67  10 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
225 401 260 
  1   2   3 
225 401 260 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5   6   7 
267 171 147 227 209  52  20 
  1   2   3   4   5   6   7 
267 171 147 227 209  52  20 
[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   5   6 
140 274 211 218 187  47 
  1   2   3   4   5   6 
140 274 211 218 187  47 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6   7   8   9 
 68 124 187 188  73 117 163  73  84 
  1   2   3   4   5   6   7   8   9 
 68 124 187 188  73 117 163  73  84 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5   6 
135  94  59 121 145 114 
  1   2   3   4   5   6 
135  94  59 121 145 114 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
318 233 117 
  1   2   3 
318 233 117 
[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 1097 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=146,	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=726,	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=12,	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=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            2576    735    
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
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 1097 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=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
281 635 138  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
281 635 138  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
281 635 138  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
281 635 138  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
516 364 120  77 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
516 364 120  77 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
516 364 120  77 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
516 364 120  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 193  35
  subtype2  97  20
  subtype3 141  28
subtype1 subtype2 subtype3 
     228      117      169 
subtype1 subtype2 subtype3 
      35       20       28 
$subtype1
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A7-A0CD TCGA-A8-A06T TCGA-A8-A084 TCGA-A8-A08S 
       63.12        88.60        38.30        53.06        15.06        33.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-AO-A0JI 
       33.01        17.95         1.02        49.05        29.98        50.24 
TCGA-B6-A0I8 TCGA-BH-A18H TCGA-C8-A1HL TCGA-E2-A15O TCGA-E2-A1BC TCGA-A1-A0SD 
       24.62        21.44        10.42        50.79        16.47        14.37 
TCGA-A1-A0SM TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
        7.96       143.15       121.94        77.19        75.25         5.19 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU 
       61.58        25.22       101.72        74.40        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0SU TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YF 
       31.82        54.64        49.84        17.46        32.55        50.47 
TCGA-A2-A0YI TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A8-A06O TCGA-A8-A06P 
       49.48        35.47        37.45        25.15        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        26.01         1.02         9.01        43.00        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
       12.00        32.05        10.98         7.99         9.99        45.07 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       31.00       112.08        40.01        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00        50.04         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
        0.99        12.00        19.04        27.02        17.03        38.04 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY 
        6.44         5.65         7.00         7.04         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03T 
        0.33         5.33        80.28        66.77        95.70        69.83 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JM 
       44.42        21.40        26.04        20.32        22.36        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G 
      113.62       108.72        98.27        77.98        70.42        53.88 
TCGA-AO-A12H TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AL 
       40.57        24.79         5.26       107.24       134.14        97.68 
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-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG 
       65.52       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        79.46        18.35       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-BH-A0AU TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.27        68.94        62.93        37.74        39.16        70.22 
TCGA-BH-A0B8 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       51.58        37.22        18.21        85.87        77.75        49.94 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 
       46.39        90.97        81.73        38.01         3.22        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       14.30        44.81        24.49        10.78        15.16        63.39 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HO 
       24.56        23.08        41.00        26.50        20.38         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       36.85        12.89        51.32        27.25        50.79        23.93 
TCGA-BH-A0W4 TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S 
       24.95        20.12        26.66        37.74        30.28        66.05 
TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-C8-A12M TCGA-C8-A12N 
        7.36       113.82        82.85        12.00        11.77        11.77 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HI TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 
       12.66        48.53        11.28        12.95        13.25        43.00 
TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       83.54        34.42        40.41        37.51        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       44.68        38.24        33.17        75.98        34.26        32.02 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D 
       23.24        19.43        21.04        23.87        22.82        17.29 
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-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BD 
       19.56        56.94        14.07        51.39        33.01        37.25 

$subtype2
TCGA-A8-A07E TCGA-AR-A1AR TCGA-BH-A0DO TCGA-BH-A0EA TCGA-D8-A146 TCGA-A1-A0SE 
       19.99        17.23        54.05        32.58        21.14        43.43 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04Q TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CV 
       47.24        13.68        78.41        99.12        92.48        98.99 
TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       53.13       134.40        80.28        72.00        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       99.19        50.43        44.28        20.52        18.90        20.75 
TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A8-A07G 
       25.28        19.33        48.46        34.29        33.11        18.97 
TCGA-A8-A09A TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FX 
        9.99        13.02        21.04         7.17         6.90         0.33 
TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       68.75        58.95        53.03        21.53        50.70        50.86 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A12A TCGA-AO-A12F TCGA-AQ-A04J 
       65.10        26.24        62.04       102.31        60.56        26.93 
TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A1AX 
      103.86        96.00        86.07        93.90        94.29        86.43 
TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      112.37       129.07       140.28        89.46       282.90       169.51 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       21.01       113.79        58.55        59.84        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       81.44        84.13        32.02        43.53        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0C3 
       61.68        72.23        75.48        74.14        76.60        89.06 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DS 
       77.98        67.10        29.98        13.91        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H5 TCGA-BH-A0HA 
       79.00        70.88        81.83        63.32        53.26        52.96 
TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
       23.90         5.85        13.61        42.35        44.81        32.91 
TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1F0 
       35.93        72.56        91.99        42.28        55.69        25.81 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A132 TCGA-C8-A135 TCGA-D8-A141 TCGA-D8-A142 
       12.66        12.66        12.59        12.92        20.58        13.97 
TCGA-D8-A145 TCGA-E2-A108 TCGA-E2-A14Z TCGA-E2-A15E TCGA-E2-A15I TCGA-E2-A15M 
       13.48        27.52        18.51        20.71        55.63        11.05 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B6 
       76.57        87.22        28.50 

$subtype3
TCGA-A1-A0SP TCGA-A2-A04Y TCGA-A8-A06U TCGA-A8-A08F TCGA-A8-A09I TCGA-E2-A158 
       19.20        36.13        29.03        33.01        45.07        14.79 
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       31.79        28.01        18.02        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D0 
       55.43        24.79       107.93        56.81        55.00        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW 
       34.55        33.76        79.76        63.29        27.12        44.88 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH 
       17.52        17.13         8.38        18.21        21.90        21.67 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA 
       18.61        31.73        23.77        35.31        30.61        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       31.73        20.19        17.98        31.00        17.03        53.98 
TCGA-A8-A07C TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B 
       33.99        14.01         9.99         8.98        24.99        38.01 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X 
       12.00        37.05         9.99        31.00         0.99        43.00 
TCGA-A8-A092 TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04C 
       30.97        33.07        25.02        14.01         0.99         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         7.46         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0G0 
        0.33         0.33         7.96         7.59         0.33         0.53 
TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A0J2 
        0.33         0.33         5.59        61.35        81.63        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 
       52.18        37.48        72.00        76.77        55.33       115.27 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ 
      106.78       108.03        82.68       130.09       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       84.10       109.02        23.31        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       55.86        65.36        83.87       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AY TCGA-B6-A0I2 
      101.00        99.32        41.82        61.28        33.73       143.38 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RE 
       32.58        11.90       233.62        18.77       140.88       255.68 
TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0X1 TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B9 
      212.25       100.70       245.10        20.45        39.55        51.68 
TCGA-BH-A0BG TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0DZ 
       61.51        77.95        74.14        41.75        78.28        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA 
        4.41         9.63        31.00        30.35         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18U TCGA-BH-A18V 
        4.90        90.84        55.63        37.55        51.39        51.16 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z 
       11.93        12.66        11.77        12.66        12.66        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
       12.16        13.51        12.59        12.46        12.49        10.92 
TCGA-C8-A1HG TCGA-C8-A1HM TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 
       11.34        12.33        56.81        20.88        14.17        19.20 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14X 
       46.59        40.11        47.15        40.96        38.60        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1B0 
       69.34        63.62        69.96        25.05        23.34        53.62 
TCGA-E2-A1B5 
       32.35 

subtype1 subtype2 subtype3 
    0.23     0.33     0.16 
subtype1 subtype2 subtype3 
  281.29   282.90   255.68 
subtype1 subtype2 subtype3 
   31.92    50.70    32.58 
[1] "0.2 - 281.3 (31.9)" "0.3 - 282.9 (50.7)" "0.2 - 255.7 (32.6)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1      23       19        3        1        71        55         34
  subtype2      20        9        0        0        41        20         19
  subtype3       8        7        0        0        70        38         25
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1          8          2        7       9
  subtype2          0          5        0       3
  subtype3          5         12        6       1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          23       20        8
  STAGE IA         19        9        7
  STAGE IB          3        0        0
  STAGE II          1        0        0
  STAGE IIA        71       41       70
  STAGE IIB        55       20       38
  STAGE IIIA       34       19       25
  STAGE IIIB        8        0        5
  STAGE IIIC        2        5       12
  STAGE IV          7        0        6
  STAGE X           9        3        1
[1] 11  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  64 134  23  12
  subtype2  47  51  19   1
  subtype3  21 127  18   7
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       64       47       21
  T2      134       51      127
  T3       23       19       18
  T4       12        1        7
[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 108  85  24   9
  subtype2  62  38  10   6
  subtype3  85  48  26  14
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      108       62       85
  N1       85       38       48
  N2       24       10       26
  N3        9        6       14
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1 217   8
  subtype2 113   0
  subtype3 165   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  217    8
  subtype2  113    0
  subtype3  165    7
   clus
vv  subtype1 subtype2 subtype3
  0      217      113      165
  1        8        0        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1 229   5
  subtype2 118   0
  subtype3 173   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  229    5
  subtype2  118    0
  subtype3  173    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      229      118      173
  MALE          5        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1  95 113
  subtype2  45  64
  subtype3  68  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95  113
  subtype2   45   64
  subtype3   68   87
     clus
vv    subtype1 subtype2 subtype3
  NO        95       45       68
  YES      113       64       87
[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                           199                             14
  subtype2                            84                             24
  subtype3                           163                              5
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                6
  subtype2                   0                                6
  subtype3                   1                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  2             13
  subtype2                  0              4
  subtype3                  0              4
D1V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING DUCTAL CARCINOMA         199       84      163
  INFILTRATING LOBULAR CARCINOMA         14       24        5
  MEDULLARY CARCINOMA                     0        0        1
  MIXED HISTOLOGY (PLEASE SPECIFY)        6        6        0
  MUCINOUS CARCINOMA                      2        0        0
  OTHER, SPECIFY                         13        4        4
[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"
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    13                        18
  subtype2                                0     5                         7
  subtype3                                1    16                        15
          vv
clus       WHITE
  subtype1   151
  subtype2   100
  subtype3   110
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  13        5       16
  BLACK OR AFRICAN AMERICAN              18        7       15
  WHITE                                 151      100      110
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus         0   1
  subtype1   4 152
  subtype2   2  94
  subtype3   1 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  152
  subtype2    2   94
  subtype3    1  126
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        1
  NOT HISPANIC OR LATINO      152       94      126
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1 134  23
  subtype2 219  47
  subtype3  78  13
subtype1 subtype2 subtype3 
     157      266       91 
subtype1 subtype2 subtype3 
      23       47       13 
$subtype1
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A7-A0CD TCGA-A8-A06T TCGA-A8-A08S TCGA-A8-A091 
       63.12        88.60        38.30        53.06        33.01        33.01 
TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-AO-A0JI TCGA-E2-A15O 
       17.95         1.02        49.05        29.98        50.24        50.79 
TCGA-A1-A0SD TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       14.37        13.68       121.94        77.19        75.25         5.19 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU 
       61.58        25.22       101.72        74.40        35.05        34.29 
TCGA-A2-A0SU TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YI 
       54.64        49.84        17.46        32.55        50.47        49.48 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A8-A06P TCGA-A8-A06Y 
       35.47        30.61        37.45        25.15        13.02        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-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08T TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09R TCGA-A8-A09T 
      112.08         9.99        12.00        50.04         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AN-A03Y TCGA-AN-A049 
       15.02        19.04        27.02        38.04         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0XP 
        2.96         6.44         5.65         7.00         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33         0.33        95.70        44.42        21.40        20.32 
TCGA-AO-A0J8 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12H 
       22.36       113.62       108.72        98.27        77.98        40.57 
TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A1AS TCGA-AR-A1AW TCGA-B6-A0I5 
       24.79         5.26       107.24        37.81        86.53       281.29 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RG 
      275.87       129.57        50.70       127.33       165.76        68.45 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0WT 
      234.28        81.17        78.02       263.28       102.77       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       79.46        18.35       206.86       129.70        28.27        68.94 
TCGA-BH-A0B4 TCGA-BH-A0B8 TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0DD TCGA-BH-A0DH 
       39.16        51.58        77.75        49.94        81.73        38.01 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 
       15.68        14.30        44.81        24.49        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HW 
       63.39        24.56        26.50        20.38         2.50        51.32 
TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES 
       27.25        23.93        26.66        37.74        66.05       113.82 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HI TCGA-C8-A1HN 
       11.77        11.77        12.66        48.53        11.28        12.95 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14O 
       43.00        83.54        40.41        37.51        28.44        44.68 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       38.24        33.17        32.02        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J 
       23.87        17.29        21.63        18.21        12.92        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 
        9.04        20.58        56.94        14.07        51.39        33.01 
TCGA-E2-A1BD 
       37.25 

$subtype2
TCGA-A2-A04Y TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A09I 
       36.13        29.03        19.99        15.06        33.01        45.07 
TCGA-B6-A0I8 TCGA-BH-A0DO TCGA-BH-A0EA TCGA-BH-A18H TCGA-C8-A1HL TCGA-D8-A146 
       24.62        54.05        32.58        21.44        10.42        21.14 
TCGA-E2-A1BC TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04N 
       16.47        43.43        47.24        31.79         7.96       143.15 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CV TCGA-A2-A0CW 
      101.98        55.43        99.12        92.48        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0CZ TCGA-A2-A0D1 TCGA-A2-A0EN TCGA-A2-A0EO 
       56.81        55.00        53.13        34.55       134.40        80.28 
TCGA-A2-A0EQ TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       79.76        72.00        31.82        61.94        24.72        63.29 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T6 
       27.12        44.88        44.28        17.13        20.52        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL 
       20.75        25.28        21.90        21.67        19.33        48.46 
TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       23.77        34.29        33.11        13.02         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G 
       31.00        17.03        53.98        43.00        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J 
       14.01        12.00         9.99        38.01        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00        31.00        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       41.98        12.00         9.99        33.07         1.02        25.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        14.01        12.00        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A0AJ 
       17.03         0.33         0.23         0.33         1.78         9.96 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.36         0.16         0.33         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.36         0.33         5.36         0.33        12.33 
TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J9 
       81.63        68.75        69.83        32.78        26.04        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E 
       26.24        62.04        71.80       102.31        82.68        70.42 
TCGA-AO-A12G TCGA-AQ-A04L TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       53.88       130.09        98.33       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AK TCGA-AR-A1AL 
       64.83        55.86        83.87       134.14       103.86        97.68 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV 
       96.00        86.07        93.90        41.82        94.29        61.28 
TCGA-AR-A1AX TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK 
       86.43        11.90        65.52       146.50       112.37        18.77 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       84.59       129.07       212.25       162.05       140.28       100.70 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AU TCGA-BH-A0AW 
      169.51        97.48       113.79        58.55        62.93        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B5 TCGA-BH-A0B7 
       25.55        63.09        81.44        37.74        70.22        84.13 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       37.22        32.02        18.21        43.53        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BZ 
       72.23        75.48        74.14        76.60        85.87        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        46.39        89.06        90.97        77.98        67.10 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       29.98        13.91        15.65         3.22         2.56        79.00 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       70.88        16.27        81.83        31.00        63.32        30.35 
TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HF TCGA-BH-A0HK 
       53.26        23.08        41.00        52.96        23.90         5.85 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85        12.89        50.79        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
       44.81        32.91        35.93        20.12        72.56        30.28 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       37.55         7.36        51.39        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       12.00        55.69        11.93        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.56        12.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HM 
       12.92        12.46        12.49        10.92        11.34        12.33 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        20.58        14.17        13.48 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14P 
       34.42        27.52        46.59        40.11        28.87        40.96 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A 
       75.98        34.26        18.51        69.96        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 
       22.82        20.71        55.63        11.05        19.56        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B6 
       87.22        28.50 

$subtype3
TCGA-A1-A0SP TCGA-AR-A1AR TCGA-E2-A158 TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q 
       19.20        17.23        14.79        28.01        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST 
       73.84        87.25        24.79        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-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR 
        8.98        24.99         0.99         1.71         7.46         0.33 
TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU 
        0.33         7.96         7.59         0.33         0.53         0.33 
TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 
       58.95        52.18        37.48        55.33       115.27       106.78 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
      108.03        60.56        26.93       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-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE 
       33.73       143.38        32.58       233.62       140.88       255.68 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 
       89.46       282.90        21.01       245.10        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-A18K TCGA-BH-A18Q 
        9.63         5.59        23.05         4.90        90.84        55.63 
TCGA-BH-A18V TCGA-BH-A1F0 TCGA-C8-A12V TCGA-C8-A134 TCGA-D8-A142 TCGA-D8-A147 
       51.16        25.81        12.66        12.59        13.97        19.20 
TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A1AZ 
       47.15        38.60        31.96        69.34        63.62        76.57 
TCGA-E2-A1B5 
       32.35 

subtype1 subtype2 subtype3 
    0.30     0.16     0.33 
subtype1 subtype2 subtype3 
  281.29   212.25   282.90 
subtype1 subtype2 subtype3 
  33.010   33.685   35.310 
[1] "0.3 - 281.3 (33.0)" "0.2 - 212.2 (33.7)" "0.3 - 282.9 (35.3)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1      17       13        3        1        55        38         19
  subtype2      25       14        0        0        87        56         51
  subtype3       9        8        0        0        40        19          8
          vv
clus       STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1          6          0        3       6
  subtype2          6         16        8       6
  subtype3          1          3        2       1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          17       25        9
  STAGE IA         13       14        8
  STAGE IB          3        0        0
  STAGE II          1        0        0
  STAGE IIA        55       87       40
  STAGE IIB        38       56       19
  STAGE IIIA       19       51        8
  STAGE IIIB        6        6        1
  STAGE IIIC        0       16        3
  STAGE IV          3        8        2
  STAGE X           6        6        1
[1] 11  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  47  93  13   8
  subtype2  63 159  39  11
  subtype3  22  60   8   1
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       47       63       22
  T2       93      159       60
  T3       13       39        8
  T4        8       11        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1  80  62  12   4
  subtype2 117  85  42  21
  subtype3  58  24   6   4
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       80      117       58
  N1       62       85       24
  N2       12       42        6
  N3        4       21        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1 151   4
  subtype2 256   8
  subtype3  88   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151    4
  subtype2  256    8
  subtype3   88    3
   clus
vv  subtype1 subtype2 subtype3
  0      151      256       88
  1        4        8        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"
D2V7, binary
          cls
clus         0   1
  subtype1 158   4
  subtype2 270   2
  subtype3  92   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  158    4
  subtype2  270    2
  subtype3   92    0
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      158      270       92
  MALE          4        2        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"
D2V8, binary
          cls
clus         0   1
  subtype1  65  81
  subtype2 112 132
  subtype3  31  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65   81
  subtype2  112  132
  subtype3   31   51
     clus
vv    subtype1 subtype2 subtype3
  NO        65      112       31
  YES       81      132       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                           142                              5
  subtype2                           220                             37
  subtype3                            84                              1
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                4
  subtype2                   0                                8
  subtype3                   1                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  2              9
  subtype2                  0              7
  subtype3                  0              5
D2V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING DUCTAL CARCINOMA         142      220       84
  INFILTRATING LOBULAR CARCINOMA          5       37        1
  MEDULLARY CARCINOMA                     0        0        1
  MIXED HISTOLOGY (PLEASE SPECIFY)        4        8        0
  MUCINOUS CARCINOMA                      2        0        0
  OTHER, SPECIFY                          9        7        5
[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"
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                        17
  subtype2                                1    21                        11
  subtype3                                0     3                        12
          vv
clus       WHITE
  subtype1   100
  subtype2   191
  subtype3    70
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  10       21        3
  BLACK OR AFRICAN AMERICAN              17       11       12
  WHITE                                 100      191       70
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
          cls
clus         0   1
  subtype1   1 108
  subtype2   5 189
  subtype3   1  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  108
  subtype2    5  189
  subtype3    1   75
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        1
  NOT HISPANIC OR LATINO      108      189       75
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 288  38
  subtype2 112  18
  subtype3 250  39
  subtype4 243  48
  subtype5  24   5
subtype1 subtype2 subtype3 subtype4 subtype5 
     326      130      289      291       29 
subtype1 subtype2 subtype3 subtype4 subtype5 
      38       18       39       48        5 
$subtype1
TCGA-A7-A0CD TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A08S TCGA-A8-A091 
       38.30        22.32        53.06        29.03        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-AO-A0JI TCGA-AO-A1KT 
        1.02        49.05        45.07        29.98        50.24        17.79 
TCGA-AQ-A54O TCGA-AR-A2LL TCGA-BH-A18H TCGA-C8-A1HL TCGA-E2-A15O TCGA-EW-A1J5 
       32.91        66.15        21.44        10.42        50.79        15.68 
TCGA-GM-A2DD TCGA-S3-AA12 TCGA-Z7-A8R5 TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ 
       75.02        18.87       108.07       133.05       131.67        48.46 
TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
        9.96        14.37        47.24        13.68         7.96        39.32 
TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0D4 
      121.94        55.43       114.81        75.25         5.19        25.22 
TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T3 
       80.28        74.40        35.05        34.29        31.82        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       20.75        32.55        21.90        23.77        17.36        60.72 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XV TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DC 
       42.44       105.34        32.75        26.96        30.61        29.79 
TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       25.15        20.61        10.59        14.93        13.74        17.92 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       13.02         1.02        17.98         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W 
       43.00        18.97        14.01        32.05        10.98         9.99 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       18.05        36.95        13.02        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09M 
       31.00        31.00        12.00         9.99        50.04        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       25.02         8.98        19.04        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2FO 
       21.04        27.02         5.72        99.35        26.04        74.14 
TCGA-AC-A3QQ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VB 
       24.13        29.26        16.80        11.44        12.26         8.22 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       20.19         0.33         0.33         0.23         0.62         2.96 
TCGA-AN-A0FD TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XS 
        6.44         0.33         0.36         0.33         5.36         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J2 
        5.59        80.28        81.63        95.70        69.83        32.78 
TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JM TCGA-AO-A12E 
       21.40        72.00        76.77        26.24        71.80        70.42 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TZ 
       61.87        11.51        24.79        15.62        98.33       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A24L 
       83.87       134.14       103.86        93.90        61.28        94.22 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A255 
      112.77       105.27       105.30        50.96        89.00        71.05 
TCGA-AR-A2LK TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RO 
       54.21        39.39        11.90        68.45        81.17       162.05 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 
       79.46        18.35       113.79       139.17       170.17        68.12 
TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ 
       62.93        39.16        76.60        77.75        49.94        74.14 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       89.06        90.97        81.73        77.98        67.10        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H0 
       13.91        78.28         3.22        14.30        63.32        15.16 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       23.08        52.96        26.50        51.32        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R 
       23.93        44.81        35.93        26.66        37.74        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EW TCGA-BH-A1F2 
       66.05        51.39        69.93       113.82        55.69        31.53 
TCGA-BH-A1FD TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A42T 
       33.17        63.35        45.63        28.14        83.31        10.52 
TCGA-BH-A5J0 TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       23.51        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HN 
       48.53        12.59        12.46        11.34        12.03        12.95 
TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 
       12.33        12.36        15.45        16.87        24.56        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       13.02        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI 
       17.49        55.50        15.78        18.15        18.90        18.97 
TCGA-D8-A1JT TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XS 
       13.32        23.90        27.58        17.16        15.22        16.31 
TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G 
       16.64        16.54        15.52        14.24        14.14        13.45 
TCGA-D8-A27I TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A107 
       14.43        17.06        10.09        12.26        43.00        34.42 
TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
       46.59        44.68        40.96        33.17        75.98        34.26 
TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       32.02        69.96        23.34        20.71        21.63        12.92 
TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE 
        9.04        19.56        56.94        14.07        51.39        77.65 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1LA TCGA-E2-A1LL TCGA-E2-A56Z 
       70.36        33.73        22.19        24.59        43.04         8.28 
TCGA-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ 
       34.29        36.82        36.56        35.24         9.86        24.82 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
       34.95         6.12         3.02        11.15        48.23        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 
       46.65         6.58        21.27        47.64        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       39.09        38.37        41.03        38.99        12.33        29.72 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OY 
       23.84        25.81        26.40        16.57        28.77        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1PD TCGA-EW-A2FR TCGA-EW-A2FS 
       40.41        41.13        23.11        13.94        55.00        52.73 
TCGA-EW-A2FW TCGA-EW-A424 TCGA-EW-A6SA TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A6FQ 
       22.09        23.51        16.77        86.96        15.32         2.63 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A66O TCGA-OL-A66P TCGA-PE-A5DC 
       19.53        12.36        22.32        17.36        14.07        47.01 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-UU-A93S TCGA-V7-A7HQ 
       18.81        18.48        21.07        17.39         3.81        66.84 
TCGA-XX-A899 TCGA-Z7-A8R6 
       15.35       107.05 

$subtype2
TCGA-A2-A0CQ TCGA-A7-A3J1 TCGA-A8-A084 TCGA-A8-A093 TCGA-AC-A5XS TCGA-AQ-A54N 
       88.60        11.28        15.06        17.95        19.33         2.56 
TCGA-AQ-A7U7 TCGA-AR-A5QM TCGA-BH-A0EA TCGA-D8-A146 TCGA-E2-A1L8 TCGA-E2-A2P5 
       19.20        73.35        32.58        21.14        73.64        26.99 
TCGA-EW-A1P3 TCGA-3C-AALK TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SQ 
       52.96        47.61        43.43        48.10        20.88        18.21 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0T4 TCGA-A2-A25C TCGA-A2-A3XU TCGA-A2-A4S2 
       77.19        98.99        20.52        17.19        29.98        21.14 
TCGA-A7-A0DB TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07Z TCGA-A8-A099 
       33.11        14.70        26.01        18.97        45.07         9.99 
TCGA-A8-A09B TCGA-A8-A09W TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A3BB TCGA-AC-A3OD 
       12.00         0.99        22.95        73.91        32.45        14.83 
TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AN-A0FK TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
       17.42         1.68         7.00        12.33         0.30         0.33 
TCGA-AO-A03N TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A128 TCGA-AO-A12A 
       66.77        20.32        53.03        21.53       106.78       102.31 
TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A5QP TCGA-B6-A0IB 
        5.26        37.81        50.89         2.76        38.96       129.57 
TCGA-B6-A0IH TCGA-B6-A0RP TCGA-B6-A1KI TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B0 
      112.37       102.77        73.51       103.63        71.15        81.44 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0DS 
       70.22        37.22        21.70        46.39        15.65         2.56 
TCGA-BH-A0E9 TCGA-BH-A0GZ TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HP TCGA-BH-A0HQ 
       81.83        10.78        41.00        20.38        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A1EV TCGA-BH-A202 
       12.89        32.91        90.84        30.28        12.00        26.14 
TCGA-BH-A28Q TCGA-BH-A6R8 TCGA-C8-A1HI TCGA-C8-A274 TCGA-C8-A3M7 TCGA-D8-A1J8 
       36.79         9.63        11.28        16.70        33.99        14.17 
TCGA-D8-A1JA TCGA-D8-A1JN TCGA-D8-A1XB TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
       16.50        20.38        18.15        14.73        55.30        15.85 
TCGA-D8-A1XU TCGA-D8-A1Y1 TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A73X TCGA-E2-A10B 
       12.99         9.93        13.08        12.53        25.22        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15G 
       28.44        28.87        38.24        23.24        19.43        18.21 
TCGA-E2-A1BD TCGA-E9-A1N6 TCGA-E9-A1NH TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A1RB 
       37.25        22.29        18.94         2.56        45.01        32.09 
TCGA-E9-A1RD TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A6HE TCGA-EW-A1IW 
        1.12         7.13        38.07        30.44        27.85        12.20 
TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1OX TCGA-EW-A1PC TCGA-GM-A3NW TCGA-GM-A3XN 
        8.48        18.90        29.95         6.15       110.50        66.38 
TCGA-LD-A66U TCGA-LL-A6FP TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5RV TCGA-OL-A66K 
       21.24        22.26        17.49        27.91        34.92        41.92 
TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-WT-AB44 
        8.91        64.21        86.96        29.03 

$subtype3
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A2-A25A 
       48.56        48.36        63.12        36.13        19.56       107.70 
TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A426 TCGA-A7-A5ZX TCGA-AC-A3W6 
       23.61        31.36        24.26        11.97        11.05        19.79 
TCGA-AC-A5EI TCGA-AR-A1AM TCGA-BH-A0DO TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-E2-A1BC 
       14.53        98.33        54.05        89.16         9.70        16.47 
TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-OL-A5RU 
       85.35        13.22        24.95        29.23        25.05        40.08 
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04W 
       11.44         8.52        14.27       143.15        78.41       101.98 
TCGA-A2-A0CK TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      136.73        92.48       107.93        61.58       101.72       134.40 
TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0SY 
      118.45        72.00        61.94        24.72        54.64        44.28 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK 
       17.46        18.90        25.28        50.47        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25F TCGA-A2-A3KC 
       48.46        22.45        16.47        52.47        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       39.65        56.28        50.37        24.39        21.30        23.21 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A13H TCGA-A7-A3IY TCGA-A7-A3J0 
       34.29        35.47        37.45        29.56        11.34        10.29 
TCGA-A7-A3RF TCGA-A7-A5ZW TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08Z 
       13.41        10.72        12.00         7.99         0.99        40.01 
TCGA-A8-A095 TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0AD TCGA-AC-A2B8 TCGA-AC-A2FB 
       41.98        15.02        14.01        38.04        22.26        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QI TCGA-AC-A3HN 
       86.66        90.71        60.92        87.12        19.33        16.31 
TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        25.05        14.99        15.48        23.24        24.79 
TCGA-AC-A6IV TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FN 
       18.67         1.32         2.30         0.33         5.65         7.17 
TCGA-AN-A0FS TCGA-AN-A0XV TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JC 
        6.90         5.33        58.95        26.04        22.36        50.86 
TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12H 
       65.10        62.04       113.62       108.72        98.27        40.57 
TCGA-AO-A1KO TCGA-AR-A0TX TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX 
       20.45        64.83        97.68        86.07        94.29        86.43 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LE 
      120.33        99.78       118.59        98.76        93.30       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN 
       20.25        86.53        63.62        38.17        40.54        33.30 
TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IK TCGA-B6-A0IN 
       10.59       281.29       275.87        50.70        18.77        84.59 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT 
      129.07       234.28        78.02       263.28       140.28        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
      169.51        97.48       188.68       206.86       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-BH-A0AZ TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BM 
       68.94        58.55        63.09        32.02        18.21        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0DH TCGA-BH-A0DT TCGA-BH-A0DV 
       72.23        74.14        85.87        38.01        79.00        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0H3 
       70.88        16.27        15.68        44.81        31.00        63.39 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0W4 TCGA-BH-A0W5 
       53.26        24.56         5.85         2.50        24.95        42.35 
TCGA-BH-A18G TCGA-BH-A18M TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1FB 
        4.90        72.56        82.85        42.28        49.58       120.62 
TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A28O TCGA-BH-A2L8 
      122.83        55.00        53.98        55.50        36.82        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      110.60        20.88         5.26        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A275 
       11.77        12.66        12.33        20.25        12.95         0.03 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A1JH TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 
       20.58        13.48        14.01        12.20        14.70        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XM TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K 
       25.74        12.39        17.69        15.16        17.42        48.03 
TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       16.41         1.61        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A14U TCGA-E2-A156 TCGA-E2-A15D 
       12.66        27.52        40.41        43.33        23.87        17.29 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       55.63        53.92        20.58        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU 
       28.50        37.41        28.44        59.18         3.88        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A2P6 TCGA-E2-A3DX 
       54.18        19.66        75.81        28.90        34.55        43.56 
TCGA-E2-A570 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R0 
       30.61        34.82        32.88        41.62        25.84        28.27 
TCGA-E9-A227 TCGA-E9-A22H TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 
       32.05        40.50         1.94        24.56         9.47        32.91 
TCGA-E9-A54X TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 
       23.90        39.72        18.21        13.25        39.78        30.08 
TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A3E8 TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.52        34.55        34.03        31.30        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY 
       79.10        85.15       115.69       106.06       101.62        38.20 
TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       43.73        72.03        13.55        18.12        62.47        11.84 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO TCGA-MS-A51U TCGA-OK-A5Q2 
       13.28        10.62        17.06        14.47        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J 
       36.30        31.99        28.87        24.72        26.70        65.62 
TCGA-OL-A66L TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY TCGA-S3-AA0Z TCGA-S3-AA11 
       42.77        19.73        40.11         0.26        20.68        13.84 
TCGA-S3-AA15 
       17.26 

$subtype4
TCGA-A1-A0SP TCGA-A7-A26I TCGA-A8-A07E TCGA-A8-A08F TCGA-AC-A3W5 TCGA-AC-A62X 
       19.20        21.73        19.99        33.01        16.57        13.71 
TCGA-AQ-A0Y5 TCGA-AR-A1AR TCGA-AR-A2LR TCGA-BH-A0B6 TCGA-E2-A158 TCGA-LL-A5YP 
        5.65        17.23        57.27        81.63        14.79        14.79 
TCGA-S3-AA17 TCGA-WT-AB41 TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T 
       13.94        52.96        31.79        28.01        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       87.25        99.12        24.79       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       34.55        33.76        79.76        63.29        99.19        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE 
       44.88        50.43        17.52        17.13         8.38        18.21 
TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT 
       21.67        18.61        31.73        19.20        33.93        91.07 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CE 
       47.31        35.93        50.83         7.30        21.90        35.31 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        31.73        20.19        23.74        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-A09N TCGA-A8-A0A7 
        9.99         0.99        43.00        30.97         1.02         0.99 
TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5XU 
       17.03        19.23        73.05        33.04        14.66        14.96 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.03         1.12         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        7.46         0.16         0.33         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XT 
        7.59         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JB 
        0.33        61.35        44.42        52.18        37.48        50.70 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
       55.33       115.27       108.03        82.68        60.56        53.88 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT 
       82.62        26.93       130.09       140.55        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 
       75.22        98.93        55.86        65.36       133.22       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AW 
      125.16       108.36       101.00        96.00        99.32        86.53 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24Z 
       33.73       160.90       104.28        97.84       102.84        98.66 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IE 
       99.62        85.64        93.83        77.62       143.38        65.52 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH 
      146.50       233.62       165.76       140.88       255.68       212.25 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A3ZX 
      100.70       282.90        21.01       245.10       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
        7.07        74.99        18.84        59.84        20.45        25.55 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       39.55        84.13        51.68        43.53        61.51        74.89 
TCGA-BH-A0BP TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB 
       75.48        77.95        41.75         4.41         9.63        24.49 
TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18J TCGA-BH-A18Q TCGA-BH-A18T 
       30.35         5.59        23.05        20.12        55.63         7.36 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 
       51.16        91.99        17.69        25.81        97.48        25.08 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       74.73        33.99        72.07        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       18.64        11.93        11.77        12.56        12.16        13.51 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM 
       12.59        12.92        12.49        10.92         0.16        12.33 
TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
       12.53         9.76        14.43        20.88        13.97        14.17 
TCGA-D8-A147 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       19.20        12.03        53.00        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       19.40        21.01        18.58        21.83        14.50        19.92 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M 
       16.41        43.04        15.32        16.04        13.05        13.48 
TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       47.15        38.60        31.96        69.34        18.51        63.62 
TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1II 
       21.04        25.05        11.05        76.57        53.62        33.70 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 
       60.99        60.36       106.75       102.61        34.92        38.76 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1RH TCGA-E9-A226 
       17.69        34.16        36.20        39.55        46.59        34.45 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FK 
       41.72        40.73        20.12         0.69        30.18        26.70 
TCGA-E9-A5FL TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P8 
        0.79        25.94        22.82        29.82        18.48         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A3U0 
       18.90        19.99        14.43        19.96        25.91        17.49 
TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       17.52        15.22        24.99        33.21         7.40       109.87 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A7W5 TCGA-LL-A441 
       70.85        72.10        69.30         2.60         7.10        32.75 
TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 
       14.70        16.08        15.68         7.46        19.59        58.52 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LX TCGA-PL-A8LZ 
       36.36        20.38        23.47        28.21         0.16         9.93 
TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-XX-A89A 
       19.27        17.03        16.04 

$subtype5
TCGA-A7-A26H TCGA-E2-A1LG TCGA-LL-A740 TCGA-W8-A86G TCGA-A2-A1FV TCGA-A2-A1G0 
       23.80        50.07        14.50        11.41        23.47        20.25 
TCGA-A2-A25D TCGA-A8-A06P TCGA-A8-A08C TCGA-A8-A08T TCGA-AC-A3EH TCGA-AC-A6IW 
       18.15        13.02        28.96       112.08         6.48        13.58 
TCGA-AO-A03R TCGA-AO-A1KP TCGA-AQ-A1H3 TCGA-B6-A0IM TCGA-B6-A1KC TCGA-B6-A401 
       68.75        97.08        32.52       127.33        43.59        85.35 
TCGA-BH-A1FC TCGA-C8-A12X TCGA-D8-A1X6 TCGA-E2-A10C TCGA-E2-A15C TCGA-E2-A1LK 
      114.15        12.66        17.79        40.11        22.82         8.75 
TCGA-E9-A1NE TCGA-GM-A2DC TCGA-JL-A3YX TCGA-OL-A5DA TCGA-OL-A66N 
       35.77        83.34        11.57        58.62        26.04 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.30     0.03     0.03     6.48 
subtype1 subtype2 subtype3 subtype4 subtype5 
  170.17   129.57   281.29   282.90   127.33 
subtype1 subtype2 subtype3 subtype4 subtype5 
  26.810   23.095   32.910   25.910   26.040 
[1] "0.2 - 170.2 (26.8)" "0.3 - 129.6 (23.1)" "0.0 - 281.3 (32.9)"
[4] "0.0 - 282.9 (25.9)" "6.5 - 127.3 (26.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      23       27        2        1       102        74         1
  subtype2       9        8        0        1        38        37         0
  subtype3      36       32        4        3        85        64         1
  subtype4      20       15        0        1       116        70         0
  subtype5       1        1        0        0        11         8         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         62         12         15        6       5
  subtype2         16          5         12        2       1
  subtype3         37          4         19        2       5
  subtype4         38          6         14        9       2
  subtype5          2          0          5        1       0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          23        9       36       20        1
  STAGE IA         27        8       32       15        1
  STAGE IB          2        0        4        0        0
  STAGE II          1        1        3        1        0
  STAGE IIA       102       38       85      116       11
  STAGE IIB        74       37       64       70        8
  STAGE III         1        0        1        0        0
  STAGE IIIA       62       16       37       38        2
  STAGE IIIB       12        5        4        6        0
  STAGE IIIC       15       12       19       14        5
  STAGE IV          6        2        2        9        1
  STAGE X           5        1        5        2        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  85 194  35  15
  subtype2  22  83  19   7
  subtype3 105 134  49   6
  subtype4  54 199  29  11
  subtype5   8  15   5   1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       85       22      105       54        8
  T2      194       83      134      199       15
  T3       35       19       49       29        5
  T4       15        7        6       11        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 136 117  49  19
  subtype2  57  44  12  16
  subtype3 147 102  18  21
  subtype4 156  83  38  16
  subtype5  10  12   2   5
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0      136       57      147      156       10
  N1      117       44      102       83       12
  N2       49       12       18       38        2
  N3       19       16       21       16        5
[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 281   7
  subtype2 102   2
  subtype3 241   2
  subtype4 244  10
  subtype5  21   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  281    7
  subtype2  102    2
  subtype3  241    2
  subtype4  244   10
  subtype5   21    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      281      102      241      244       21
  1        7        2        2       10        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"
D3V7, binary
          cls
clus         0   1
  subtype1 318  12
  subtype2 131   0
  subtype3 295   0
  subtype4 294   0
  subtype5  29   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  318   12
  subtype2  131    0
  subtype3  295    0
  subtype4  294    0
  subtype5   29    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      318      131      295      294       29
  MALE         12        0        0        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 135 167
  subtype2  42  79
  subtype3 134 136
  subtype4 111 152
  subtype5  15  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  135  167
  subtype2   42   79
  subtype3  134  136
  subtype4  111  152
  subtype5   15   13
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO       135       42      134      111       15
  YES      167       79      136      152       13
[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                           262
  subtype2                          0                            78
  subtype3                          0                           152
  subtype4                          1                           259
  subtype5                          0                            17
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             41                   0
  subtype2                             45                   0
  subtype3                             97                   0
  subtype4                             10                   5
  subtype5                              8                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     2                               11
  subtype2                     0                                4
  subtype3                     2                               10
  subtype4                     5                                5
  subtype5                     0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  4             10
  subtype2                  1              3
  subtype3                 11             23
  subtype4                  0              8
  subtype5                  1              2
D3V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA         262       78      152      259       17
  INFILTRATING LOBULAR CARCINOMA         41       45       97       10        8
  MEDULLARY CARCINOMA                     0        0        0        5        1
  METAPLASTIC CARCINOMA                   2        0        2        5        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       11        4       10        5        0
  MUCINOUS CARCINOMA                      4        1       11        0        1
  OTHER, SPECIFY                         10        3       23        8        2
[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    24                        49
  subtype2                                0     7                        14
  subtype3                                0    11                        36
  subtype4                                1    16                        75
  subtype5                                0     2                         7
          vv
clus       WHITE
  subtype1   212
  subtype2   101
  subtype3   231
  subtype4   183
  subtype5    17
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                  24        7       11       16        2
  BLACK OR AFRICAN AMERICAN              49       14       36       75        7
  WHITE                                 212      101      231      183       17
[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  10 261
  subtype2   4  99
  subtype3  13 246
  subtype4  12 242
  subtype5   0  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  261
  subtype2    4   99
  subtype3   13  246
  subtype4   12  242
  subtype5    0   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           10        4       13       12        0
  NOT HISPANIC OR LATINO      261       99      246      242       26
[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 200  23
  subtype2 149  35
  subtype3 128  17
  subtype4 117  23
  subtype5  84   4
subtype1 subtype2 subtype3 subtype4 subtype5 
     223      184      145      140       88 
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       35       17       23        4 
$subtype1
TCGA-5L-AAT0 TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-BH-A1F5 
       48.56        31.36        22.32        11.28        11.97        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A572 TCGA-EW-A1J5 
        9.70        10.42        16.47        73.64        39.72        15.68 
TCGA-EW-A1P3 TCGA-LL-A442 TCGA-LL-A50Y TCGA-S3-AA12 TCGA-3C-AAAU TCGA-3C-AALI 
       52.96        29.23        25.05        18.87       133.05       131.67 
TCGA-4H-AAAK TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SQ 
       11.44        43.43        14.27        47.24        20.88        18.21 
TCGA-A2-A04R TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0EU TCGA-A2-A0YC TCGA-A2-A0YF 
      121.94       136.73       114.81        34.29        32.55        50.47 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E 
       23.47        60.72        20.25        42.44        17.19       105.34 
TCGA-A2-A4S2 TCGA-A7-A0D9 TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 
       21.14        37.45        20.61        10.59        13.41        14.70 
TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A08O TCGA-A8-A0AD TCGA-AC-A23E 
       13.74        14.73        10.42        31.00        38.04        22.95 
TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QI TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3YJ 
       99.35        60.92        19.33        24.13        14.99        24.79 
TCGA-AC-A6NO TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        1.68         5.36         0.30         0.33         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A0JD TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B 
       66.77        72.00        62.04       113.62       108.72        98.27 
TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A1H2 TCGA-AR-A0TR TCGA-AR-A1AK 
       77.98        97.08        61.87        15.62         5.26       103.86 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24V 
       97.68        96.00        37.81        94.22       120.33       105.30 
TCGA-AR-A24Z TCGA-AR-A2LE TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
       98.66       166.42        68.45       234.28        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X4 
      162.05       102.77       188.68        79.46       206.86        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A408 
       68.94        58.55        43.59        73.51       170.17        68.12 
TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B8 TCGA-BH-A0BA TCGA-BH-A0BC 
       62.93        63.09        70.22        51.58        37.22        32.02 
TCGA-BH-A0BM TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0H0 
       61.68        85.87        77.75        15.65         3.22        15.16 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF 
       24.56        23.08        41.00        52.96        26.50        23.90 
TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A1EO TCGA-BH-A1ES 
       20.38        16.96        23.93        24.95        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A204 
       82.85        49.58        63.35        55.00        53.98        83.31 
TCGA-BH-A28Q TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A1HG TCGA-C8-A26W TCGA-C8-A26Z 
       36.79        23.51         9.63        11.34        12.53        15.45 
TCGA-C8-A273 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS 
       16.87        15.78        18.15        18.90        18.97        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB 
       13.32        17.79        16.73        25.74        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV 
       12.39        19.92        55.30        15.85        16.31        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.54        15.52        13.08        12.53        33.37        18.51 
TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A15I 
       83.54        34.42        37.51        28.44        28.87        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A1B4 TCGA-E2-A1IE TCGA-E2-A1IL TCGA-E2-A1IN 
       53.92         9.04        33.01        77.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N3 
       60.99        11.08        19.66         8.28        30.61        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 
       32.88        36.82        18.94         9.86        28.27         2.56 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
       32.09         1.12        21.27        34.45        32.05        37.74 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54Y 
       41.72        40.50         7.13        38.07        32.91        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1J3 
       25.81        26.40        27.85        39.72        18.90        16.57 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PE 
       28.77        29.85        41.13        23.11        18.48        10.52 
TCGA-EW-A2FW TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       22.09        15.22        31.30        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-OL-A66H TCGA-OL-A66J 
       21.24        13.28        22.26         2.63        26.70        65.62 
TCGA-OL-A66O TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-S3-AA11 TCGA-S3-AA14 TCGA-V7-A7HQ 
       17.36        19.73        40.11        13.84        17.39        66.84 
TCGA-Z7-A8R6 
      107.05 

$subtype2
TCGA-A2-A1G4 TCGA-A7-A26H TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AR-A2LL 
       19.56        23.80        50.24        17.79         5.65        66.15 
TCGA-AR-A5QM TCGA-E2-A2P5 TCGA-LL-A740 TCGA-S3-AA17 TCGA-3C-AALJ TCGA-3C-AALK 
       73.35        26.99        14.50        13.94        48.46        47.61 
TCGA-5T-A9QA TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CT TCGA-A2-A0SV 
        9.96        48.10        13.68        39.32        75.25        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0YG TCGA-A2-A0YT 
       44.88        44.28        20.52        18.90        21.90        23.77 
TCGA-A2-A1FW TCGA-A2-A25D TCGA-A2-A3XV TCGA-A7-A13F TCGA-A7-A4SF TCGA-A8-A075 
       17.36        18.15        32.75        25.15        17.92        17.03 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FM TCGA-AC-A3EH TCGA-AC-A4ZE 
       19.23         5.72        22.26        26.04         6.48        29.26 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A8OP 
       16.80        14.96        11.44        12.26         8.22        20.19 
TCGA-AC-A8OS TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A0JA 
        2.30         0.33        12.33         5.33        80.28        21.53 
TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KS 
       76.77        26.24        71.80        70.42        53.88        11.51 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TZ 
       24.79       130.09        98.33        75.22        98.93       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A24H 
       83.87       134.14        93.90        41.82        61.28       160.90 
TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A5QN 
       99.78       112.77        89.00        71.05        54.21        33.30 
TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0WW TCGA-B6-A1KN TCGA-B6-A40B TCGA-B6-A40C 
       18.77        81.17        18.35       139.17       103.63        71.15 
TCGA-BH-A0AW TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DS 
       20.45        74.14        81.73        38.01        13.91         2.56 
TCGA-BH-A0E2 TCGA-BH-A0HK TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A1EN TCGA-BH-A1EV 
       14.30         5.85        27.25        50.79        69.93        12.00 
TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM 
       55.69        17.69        31.53        25.08        33.17        45.63 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A42T TCGA-BH-AB28 TCGA-C8-A1HM TCGA-C8-A1HN 
       26.14        38.60        10.52         9.44        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 
       12.33        20.25        16.70         0.03        24.56        12.95 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF 
       12.49        19.46        14.17        17.49        16.50        12.03 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XF 
       53.00        20.09        20.38        18.58        23.90        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G 
       21.83        12.99        15.32         9.93        14.14        13.45 
TCGA-D8-A27N TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10C 
       17.06        12.26        12.66        43.00        46.59        40.11 
TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A2P6 TCGA-E2-A576 
       37.25        70.36        60.36        28.90        34.55        34.29 
TCGA-E2-A9RU TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       17.69        36.56        35.24         3.02        11.15        48.23 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A247 
       40.24        46.65         6.58        42.25        38.37        38.99 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1IW TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       12.33        29.72        12.20        25.94        29.95        40.41 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       18.90         6.15        52.73        34.03        17.52        23.51 
TCGA-EW-A6SA TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DL TCGA-GM-A3NW 
       16.77         7.40        59.57        83.34       115.69       110.50 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 
       17.06        15.32        12.36        17.49        27.91        31.99 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DC TCGA-PE-A5DD TCGA-S3-A6ZF 
       41.92        42.77        26.04        47.01        64.21        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.48        21.07        17.03         3.81 

$subtype3
TCGA-5L-AAT1 TCGA-A2-A25A TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AQ-A7U7 TCGA-AR-A1AM 
       48.36       107.70        19.79        19.33        19.20        98.33 
TCGA-BH-A0B6 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LL-A440 TCGA-OL-A5RU TCGA-WT-AB41 
       81.63        75.02        85.35        24.95        40.08        52.96 
TCGA-Z7-A8R5 TCGA-A2-A0CR TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ST TCGA-A2-A0T1 
      108.07       107.93       134.40       118.45        99.19        17.13 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A25F TCGA-A2-A3XW 
       21.67        49.48        19.33        48.46        10.59        56.28 
TCGA-A2-A3XZ TCGA-A2-A4S3 TCGA-A7-A3IY TCGA-A7-A4SA TCGA-AC-A23G TCGA-AC-A2FB 
       50.37        21.90        11.34        14.93        73.91        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FO TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3YI 
       86.66        90.71        74.14        14.66        32.45        23.24 
TCGA-AC-A6IV TCGA-AC-A8OQ TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03U TCGA-AO-A0JC 
       18.67         1.12         5.59        61.35        58.95        50.86 
TCGA-AO-A0JF TCGA-AO-A128 TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AO 
       65.10       106.78       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       102.84        93.30 
TCGA-AR-A2LH TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QQ TCGA-B6-A0RT 
       20.25        38.17        39.39        40.54        10.59        89.46 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-BH-A0BF TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DV 
       37.87        85.35        43.53        41.75        89.06        67.86 
TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A1EU TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE 
        5.59        42.35        42.28        25.81       120.62        74.73 
TCGA-BH-A1FU TCGA-BH-A209 TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 
       55.50       130.16        20.12       110.60        20.88         5.26 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A8HP 
       18.87        21.76        12.36         9.76        33.99        13.02 
TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M 
       13.41        55.50        14.24        14.43        16.41        13.48 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A108 TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 
       21.67        16.18        27.52        87.22        32.35        28.50 
TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1LA TCGA-E2-A3DX 
       37.41        33.70        28.44        59.18        24.59        43.56 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A22A 
       39.55        35.77        25.84        24.82         6.12        39.09 
TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3QA TCGA-E9-A3X8 
       41.03        20.12         1.94         9.47        30.18        30.44 
TCGA-E9-A5FK TCGA-EW-A1IZ TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PF TCGA-EW-A1PG 
       26.70        18.21        39.78        30.08        14.43        34.55 
TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       25.91        17.49       216.76        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DN TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-LD-A7W5 TCGA-LD-A9QF 
       86.96       101.62        66.38        72.03         7.10        10.62 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 
       32.75        14.70        14.47        19.53        22.39         2.10 
TCGA-OL-A5RY TCGA-OL-A66P TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-AA15 TCGA-XX-A899 
       24.72        14.07        86.96         9.93        17.26        15.35 
TCGA-XX-A89A 
       16.04 

$subtype4
TCGA-A1-A0SP TCGA-A7-A26F TCGA-A7-A26I TCGA-AC-A3W5 TCGA-AC-A5EI TCGA-AC-A62X 
       19.20        24.26        21.73        16.57        14.53        13.71 
TCGA-AQ-A54N TCGA-AR-A1AR TCGA-AR-A2LR TCGA-E2-A1LG TCGA-LL-A5YP TCGA-A1-A0SB 
        2.56        17.23        57.27        50.07        14.79         8.52 
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T7 
       31.79        28.01        50.43        17.52         8.38        20.75 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT 
       18.21        18.61        31.73        19.20        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 
       29.98        47.31        35.93        50.83        24.39        26.96 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       31.73        20.19        23.74        14.50        21.17        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A6IW 
       10.29         9.37         8.75        73.05        33.04        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-AR-A0TP TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       20.45        82.62       140.55        23.31        65.36       107.21 
TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 
      108.36        99.32        33.73       104.28        99.62        93.83 
TCGA-B6-A0I1 TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
       77.62       255.68       100.70       282.90        21.01       245.10 
TCGA-B6-A1KF TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0B3 TCGA-BH-A0B9 
      101.52         7.07        74.99        18.84        39.55        51.68 
TCGA-BH-A0E0 TCGA-BH-A0GY TCGA-BH-A0WA TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN 
        4.41        30.35        23.05        97.48       114.15        72.07 
TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A26Y 
       57.83        18.64        10.92         0.16        12.03        12.95 
TCGA-C8-A27B TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ 
       14.43        20.12        20.09        19.40        14.50        16.41 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R TCGA-E2-A14N 
       16.64        43.04        16.04        13.05        10.09        47.15 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       76.57        53.62       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       52.73        34.92        38.76        22.29        34.16        36.20 
TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A5FL TCGA-EW-A1OW 
       41.62        46.59        40.73         0.69         0.79        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A6SB 
       29.82         7.86        19.99        19.96        55.00        24.99 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       33.21       109.87        79.10        69.30         2.60        11.84 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 
       16.08        15.68         7.46        19.59        36.30        58.52 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-OL-A97C 
       36.36        22.32        20.38        23.47        28.21         8.91 
TCGA-S3-AA0Z TCGA-S3-AA10 
       20.68        19.27 

$subtype5
TCGA-A7-A13G TCGA-A7-A5ZX TCGA-AQ-A54O TCGA-LD-A74U TCGA-W8-A86G TCGA-A1-A0SM 
       23.61        11.05        32.91        13.22        11.41         7.96 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 
       54.64        17.46        25.28        22.45        16.47        52.47 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A7-A13H 
       36.23        39.65         7.30        21.30        23.21        29.56 
TCGA-A7-A3J0 TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A8-A0A6 TCGA-AC-A2FK TCGA-AC-A3HN 
       10.29        14.66        10.72        21.04        87.12        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A62Y TCGA-AC-A8OR 
       14.83        22.19        25.05        15.48        17.42         1.32 
TCGA-AQ-A1H3 TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       32.52        94.29        50.89         2.76       105.27        50.96 
TCGA-AR-A24X TCGA-AR-A254 TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A5QP TCGA-B6-A0RV 
       98.76        85.64        86.53        63.62        38.96       169.51 
TCGA-B6-A0WY TCGA-BH-A0BJ TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0E1 TCGA-BH-A0GZ 
      113.79        21.70        67.10        29.98        15.68        10.78 
TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O 
       63.39        13.61       122.83        33.99        28.14        36.82 
TCGA-C8-A1HE TCGA-C8-A1HI TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XD 
       12.33        11.28        14.01        21.01        14.70        17.16 
TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A73X 
       14.73        17.69        17.42        48.03         1.61        25.22 
TCGA-E2-A14U TCGA-E2-A1IH TCGA-E2-A1L6 TCGA-E2-A1LB TCGA-E9-A1R2 TCGA-E9-A1RA 
       43.33        33.73        54.18        75.81        34.95        45.01 
TCGA-E9-A1RI TCGA-E9-A24A TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J2 TCGA-EW-A1PD 
       47.64        24.56        23.90         8.48        13.25        13.94 
TCGA-GM-A2DM TCGA-GM-A3NY TCGA-GM-A3XG TCGA-HN-A2OB TCGA-OL-A5DA TCGA-OL-A5RV 
      106.06        38.20        43.73        62.47        58.62        34.92 
TCGA-OL-A5RX TCGA-PL-A8LX TCGA-PL-A8LY TCGA-WT-AB44 
       28.87         0.16         0.26        29.03 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.30     0.03     1.12     0.03     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  263.28   160.90   216.76   282.90   169.51 
subtype1 subtype2 subtype3 subtype4 subtype5 
  28.270   24.675   35.770   24.690   25.135 
[1] "0.3 - 263.3 (28.3)" "0.0 - 160.9 (24.7)" "1.1 - 216.8 (35.8)"
[4] "0.0 - 282.9 (24.7)" "0.2 - 169.5 (25.1)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      17       19        3        1        60        63         0
  subtype2       8       11        0        2        53        41         1
  subtype3      22       10        1        1        47        26         1
  subtype4       6        9        1        1        63        38         0
  subtype5       7       12        0        1        21        19         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         39          5         12        1       3
  subtype2         38          8         16        4       1
  subtype3         23          3          9        2       0
  subtype4         13          1          5        2       1
  subtype5         13          1         11        2       0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          17        8       22        6        7
  STAGE IA         19       11       10        9       12
  STAGE IB          3        0        1        1        0
  STAGE II          1        2        1        1        1
  STAGE IIA        60       53       47       63       21
  STAGE IIB        63       41       26       38       19
  STAGE III         0        1        1        0        0
  STAGE IIIA       39       38       23       13       13
  STAGE IIIB        5        8        3        1        1
  STAGE IIIC       12       16        9        5       11
  STAGE IV          1        4        2        2        2
  STAGE X           3        1        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  61 129  27   5
  subtype2  30 109  34  11
  subtype3  54  69  19   3
  subtype4  26  96  15   3
  subtype5  28  44  14   2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       61       30       54       26       28
  T2      129      109       69       96       44
  T3       27       34       19       15       14
  T4        5       11        3        3        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"
          vv
clus       N0 N1 N2 N3
  subtype1 86 91 29 13
  subtype2 74 59 29 17
  subtype3 69 48 18 10
  subtype4 83 40 11  6
  subtype5 37 31  8 11
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       86       74       69       83       37
  N1       91       59       48       40       31
  N2       29       29       18       11        8
  N3       13       17       10        6       11
[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"
D4V6, binary
          cls
clus         0   1
  subtype1 180   1
  subtype2 136   5
  subtype3 114   2
  subtype4 112   3
  subtype5  67   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  180    1
  subtype2  136    5
  subtype3  114    2
  subtype4  112    3
  subtype5   67    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      180      136      114      112       67
  1        1        5        2        3        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"
D4V7, binary
          cls
clus         0   1
  subtype1 222   2
  subtype2 180   4
  subtype3 145   0
  subtype4 141   0
  subtype5  85   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  222    2
  subtype2  180    4
  subtype3  145    0
  subtype4  141    0
  subtype5   85    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      222      180      145      141       85
  MALE          2        4        0        0        3
[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"
D4V8, binary
          cls
clus         0   1
  subtype1  93 116
  subtype2  74  98
  subtype3  56  80
  subtype4  58  71
  subtype5  35  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93  116
  subtype2   74   98
  subtype3   56   80
  subtype4   58   71
  subtype5   35   47
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        93       74       56       58       35
  YES      116       98       80       71       47
[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                           140
  subtype2                          0                           128
  subtype3                          0                            82
  subtype4                          1                           114
  subtype5                          0                            47
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             52                   0
  subtype2                             42                   0
  subtype3                             50                   2
  subtype4                              5                   4
  subtype5                             30                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               12
  subtype2                     0                                6
  subtype3                     3                                4
  subtype4                     6                                1
  subtype5                     0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  5             15
  subtype2                  4              4
  subtype3                  1              3
  subtype4                  0              9
  subtype5                  5              3
D4V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA         140      128       82      114       47
  INFILTRATING LOBULAR CARCINOMA         52       42       50        5       30
  MEDULLARY CARCINOMA                     0        0        2        4        0
  METAPLASTIC CARCINOMA                   0        0        3        6        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       12        6        4        1        3
  MUCINOUS CARCINOMA                      5        4        1        0        5
  OTHER, SPECIFY                         15        4        3        9        3
[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"
D4V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    10                        32
  subtype2                                0    11                        35
  subtype3                                1     7                        26
  subtype4                                0     7                        56
  subtype5                                0     3                        11
          vv
clus       WHITE
  subtype1   179
  subtype2   134
  subtype3   108
  subtype4    75
  subtype5    72
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                  10       11        7        7        3
  BLACK OR AFRICAN AMERICAN              32       35       26       56       11
  WHITE                                 179      134      108       75       72
[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"
D4V12, binary
          cls
clus         0   1
  subtype1  12 190
  subtype2  11 162
  subtype3   7 127
  subtype4   5 122
  subtype5   3  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  190
  subtype2   11  162
  subtype3    7  127
  subtype4    5  122
  subtype5    3   74
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           12       11        7        5        3
  NOT HISPANIC OR LATINO      190      162      127      122       74
[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(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 162  32
  subtype2 206  32
  subtype3  24   6
  subtype4 184  21
  subtype5 111  19
  subtype6  60   7
  subtype7   5   5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     194      238       30      205      130       67       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      32       32        6       21       19        7        5 
$subtype1
TCGA-5L-AAT1 TCGA-A7-A26F TCGA-A7-A26I TCGA-A8-A06U TCGA-AC-A62X TCGA-AO-A1KT 
       48.36        24.26        21.73        29.03        13.71        17.79 
TCGA-AQ-A54N TCGA-E2-A158 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A5YP TCGA-S3-AA17 
        2.56        14.79        85.35        13.22        14.79        13.94 
TCGA-3C-AALI TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P 
      131.67        11.44         9.96        31.79        28.01        18.02 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0EQ 
       73.84        87.25        24.79        55.00        67.33        79.76 
TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 
       99.19        27.12        44.88        50.43        17.52         8.38 
TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A0YM TCGA-A2-A25D TCGA-A2-A3XT TCGA-A2-A3XU 
       18.21        21.67        31.73        18.15        91.07        29.98 
TCGA-A7-A0CE TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VX 
       35.31        20.19        14.50        17.92        10.29        10.42 
TCGA-A8-A06X TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A08P TCGA-A8-A09M TCGA-AC-A2BK 
       31.00         9.99         8.98        31.00        33.07        73.05 
TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
       14.96        13.58         1.68         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0G0 
        7.46         0.33         0.33         0.33         7.96         0.53 
TCGA-AN-A0XU TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A124 
        0.33        81.63        32.78        37.48        72.00       115.27 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AR-A0TP 
      108.03        60.56        61.87        82.62        11.51       140.55 
TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A0U1 
      109.02        23.31        75.22        98.93        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A24U 
      134.14       125.16       108.36        86.07        99.32       102.84 
TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RU 
       93.83        10.59        32.58       233.62       140.88       282.90 
TCGA-B6-A0X1 TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0DL TCGA-BH-A0E0 
      245.10        39.55        51.68        43.53        78.28         4.41 
TCGA-BH-A0EE TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1F0 
       31.00        55.63        37.55         7.36        51.16        25.81 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A6R9 
      114.15        33.17        26.14        38.60       130.16         5.26 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A1HF TCGA-C8-A1HG 
       11.93        11.77        12.66        12.66        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A275 
        0.16        12.03        12.33        20.25        16.87         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
        9.76        24.56        14.43        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JC TCGA-D8-A1JL 
       56.81        20.88        14.17        19.20        15.78        20.09 
TCGA-D8-A1JM TCGA-D8-A1XL TCGA-D8-A1XT TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F 
       19.40        19.92        16.64        15.32        14.14        16.04 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Z TCGA-E2-A159 
       16.18        12.66        47.15        40.96        18.51        25.05 
TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1L7 TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A574 
       23.34        76.57        60.36         8.75        52.73        38.76 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       17.69        22.29        34.16        36.20        36.56        41.62 
TCGA-E9-A1RB TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5FL 
       32.09        40.73        20.12         1.94        23.84         0.79 
TCGA-EW-A1OW TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FV TCGA-EW-A6S9 
       22.82         7.86        19.99         6.15        25.91        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A3XL 
       16.77        24.99        33.21       109.87        72.10        69.30 
TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-LL-A8F5 
        7.10        10.62        32.75        14.47        19.53        19.59 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY 
       58.52        36.36        28.21        19.73         0.16         0.26 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-UL-AAZ6 TCGA-UU-A93S 
       21.07        20.68        19.27        13.84        17.03         3.81 
TCGA-XX-A899 TCGA-Z7-A8R6 
       15.35       107.05 

$subtype2
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A7-A2KD 
       63.12        36.13        88.60        19.56        38.30        22.32 
TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-AC-A5XS TCGA-AQ-A54O 
       33.01         1.02        49.05        45.07        19.33        32.91 
TCGA-BH-A0B6 TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A15O 
       81.63        89.16         9.70        10.42        21.14        50.79 
TCGA-E2-A2P5 TCGA-EW-A1J5 TCGA-LL-A442 TCGA-LL-A50Y TCGA-S3-AA12 TCGA-WT-AB41 
       26.99        15.68        29.23        25.05        18.87        52.96 
TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-A1-A0SF TCGA-A1-A0SQ TCGA-A2-A0CK TCGA-A2-A0CS 
      108.07        47.61        48.10        18.21       136.73        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 
       75.25         5.19        98.99       107.93        61.58        25.22 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 
       54.64        17.46        25.28        17.36        60.72        20.25 
TCGA-A2-A25B TCGA-A2-A4S0 TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC 
       42.44        23.21        35.47        30.61        33.11        29.79 
TCGA-A7-A13F TCGA-A7-A3IZ TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07S 
       25.15        10.59        14.70        26.01         1.02         7.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        18.05        36.95        13.02         0.99 
TCGA-A8-A08G TCGA-A8-A08T TCGA-A8-A099 TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A3TM 
       19.96       112.08         9.99        26.04        19.33        25.05 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FF 
       24.79        29.26         0.23         2.96         6.44         5.65 
TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO 
        7.00         7.04         0.36         0.33         0.33        12.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33         0.33        66.77        95.70        21.40        20.32 
TCGA-AO-A0JC TCGA-AO-A0JG TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G 
       50.86        26.24       108.72        98.27        77.98        53.88 
TCGA-AO-A12H TCGA-AQ-A1H2 TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K 
       40.57        15.62         5.26        37.81        61.28        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Z TCGA-AR-A2LK TCGA-AR-A5QN TCGA-B6-A0IB 
      120.33        99.78        98.66        54.21        33.30       129.57 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-B6-A2IU TCGA-BH-A0BS 
       81.17        78.02       102.77       129.70       170.17        85.87 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0DT TCGA-BH-A0E7 
       49.94        90.97        81.73        13.91        79.00        44.81 
TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HU TCGA-BH-A0HW 
       53.26        41.00         5.85         2.37        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1ET 
       27.25        24.95        37.74        66.05       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 
       42.28       122.83        63.35        45.63        53.98        83.31 
TCGA-BH-A28Q TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12X 
       36.79        20.88        18.87        21.76        11.77        12.66 
TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A1JE 
       11.28        12.95        15.45        12.95        13.25        18.90 
TCGA-D8-A1JI TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 
       18.97        20.38        21.01        12.20        13.32        17.79 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO 
       25.74        23.90        18.15        17.16        14.73        55.30 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y1 TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27L 
       12.99        15.16         9.93        17.42        48.03        16.41 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X TCGA-E2-A107 
        1.61        13.08        12.53        12.26        25.22        34.42 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14Q TCGA-E2-A14S 
       46.59        40.41        37.51        28.44        38.24        33.17 
TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15D 
       32.02        23.24        19.43        21.04        23.87        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       20.71        18.21        53.92         9.04        20.58        11.05 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IG 
       56.94        14.07        51.39        33.01        37.25        70.36 
TCGA-E2-A1L6 TCGA-E2-A56Z TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1R2 
       54.18         8.28        34.82        32.88        36.82        34.95 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A228 
        3.02        48.23         1.12        46.65        21.27        42.25 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS 
       38.37        41.03        40.50        38.99        24.56        29.72 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A6HE TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1OX 
       32.91        23.90        27.85        18.90        16.57        29.95 
TCGA-EW-A1P0 TCGA-EW-A2FW TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DM TCGA-GM-A2DN 
       41.13        22.09        59.57        83.34       106.06       101.62 
TCGA-LD-A7W6 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       13.28        15.32        22.26         2.63        17.49        27.91 
TCGA-MS-A51U TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66O TCGA-PE-A5DC 
       22.39        31.99        34.92        28.87        17.36        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-S3-AA14 
       64.21        86.96        18.48        17.39 

$subtype3
TCGA-AC-A3W5 TCGA-AR-A2LL TCGA-LL-A740 TCGA-A1-A0SH TCGA-A7-A4SA TCGA-A8-A06R 
       16.57        66.15        14.50        47.24        14.93        17.98 
TCGA-A8-A07I TCGA-A8-A08L TCGA-A8-A08Z TCGA-A8-A09A TCGA-A8-A09R TCGA-AC-A2QJ 
       14.01         9.99        40.01         9.99         8.98        14.66 
TCGA-AN-A0FV TCGA-AR-A1AY TCGA-BH-A0C3 TCGA-BH-A0W5 TCGA-BH-A1EN TCGA-BH-A1F8 
        0.33        33.73        89.06        42.35        69.93        25.08 
TCGA-BH-A201 TCGA-BH-A42T TCGA-C8-A12Y TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF 
       28.14        10.52        48.53        17.49        16.50        12.03 
TCGA-D8-A1JH TCGA-D8-A1JU TCGA-E2-A150 TCGA-E2-A152 TCGA-E9-A226 TCGA-LL-A5YN 
       14.01        14.70        63.62        69.96        34.45        14.70 

$subtype4
TCGA-A2-A25A TCGA-A7-A3J1 TCGA-AO-A0JI TCGA-AR-A1AM TCGA-AR-A5QM TCGA-B6-A0I8 
      107.70        11.28        50.24        98.33        73.35        24.62 
TCGA-BH-A0EA TCGA-BH-A18H TCGA-E2-A1BC TCGA-GM-A2DD TCGA-LL-A440 TCGA-OL-A5RU 
       32.58        21.44        16.47        75.02        24.95        40.08 
TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0EP 
       13.68       143.15        99.12        92.48       107.93       118.45 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0T3 TCGA-A2-A0T4 
       34.29        31.82        61.94        24.72        49.84        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT 
       18.90        20.75        49.48        19.33        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25E TCGA-A2-A3KC 
       23.47        19.20        16.47        52.47       105.34        36.23 
TCGA-A2-A3XW TCGA-A2-A4RW TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A3J0 TCGA-A7-A4SC 
       56.28         7.30        34.29        37.45        10.29        14.66 
TCGA-A8-A06P TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A08O TCGA-A8-A09B TCGA-AC-A23C 
       13.02        18.97        10.98        31.00        12.00        19.23 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A3HN 
       22.26        99.35        86.66        90.71        60.92        16.31 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A6IX TCGA-AC-A8OQ TCGA-AN-A049 TCGA-AN-A0FS 
       22.19        14.99        12.26         1.12         0.62         6.90 
TCGA-AN-A0XN TCGA-AO-A03L TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JF 
        0.33        80.28        26.04        22.36        53.03        65.10 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04L 
       62.04        71.80        70.42        20.45        97.08       130.09 
TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TZ TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       32.52        98.33       107.24       101.00       103.86        97.68 
TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24R TCGA-AR-A24T 
       93.90        94.29        94.22       118.59       112.77       105.27 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
      105.30        50.96        98.76        89.00        93.30        71.05 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        86.53        63.62        38.17        39.39        40.54 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0IO TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
       38.96       143.38       165.76       263.28       162.05       140.28 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       89.46       169.51        62.93        25.55        63.09        81.44 
TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ 
       37.74        39.16        70.22        37.22        32.02        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0DG 
       61.68        72.23        75.48        74.14        76.60        67.10 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E6 
       38.01        29.98        15.65         2.56        67.86         9.63 
TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HN TCGA-BH-A0HP 
       81.83        30.35        24.56        52.96        16.96        13.61 
TCGA-BH-A18M TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FL 
       72.56        51.39        55.69       120.62        74.73        55.00 
TCGA-BH-A42U TCGA-BH-A6R8 TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A135 TCGA-C8-A1HE 
      110.60         9.63        11.77        12.66        12.92        12.33 
TCGA-C8-A274 TCGA-C8-A3M7 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1XA TCGA-D8-A1XR 
       16.70        33.99        13.48        55.50        27.58        15.85 
TCGA-D8-A1Y0 TCGA-D8-A27G TCGA-D8-A27I TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14O 
       15.52        13.45        14.43        27.52        40.11        44.68 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15P 
       75.98        34.26        22.82        21.63        55.63        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A3DX TCGA-E9-A1NE 
       87.22        32.35         3.88        11.08        43.56        35.77 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1RA TCGA-E9-A1RH TCGA-E9-A229 
       18.94        24.82        28.27        45.01        46.59        37.74 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 
       12.33         9.47        30.44        39.72        18.21        13.25 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE 
       39.78        29.82        23.11        18.90        13.94        10.52 
TCGA-EW-A1PG TCGA-EW-A424 TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       34.55        23.51        70.85        85.15        86.96       115.69 
TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       38.20        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A73Z TCGA-OL-A5RY TCGA-OL-A66I 
       62.47        11.57        21.24         7.46        24.72        23.47 
TCGA-OL-A66J 
       65.62 

$subtype5
TCGA-A7-A26E TCGA-A7-A26H TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A09K TCGA-AC-A3W6 
       31.36        23.80        19.99        15.06        29.98        19.79 
TCGA-AC-A5EI TCGA-AQ-A7U7 TCGA-AR-A2LR TCGA-E2-A1LG TCGA-E2-A572 TCGA-EW-A1P3 
       14.53        19.20        57.27        50.07        39.72        52.96 
TCGA-W8-A86G TCGA-A2-A04Q TCGA-A2-A04W TCGA-A2-A0CZ TCGA-A2-A0D1 TCGA-A2-A0D2 
       11.41        78.41       101.98        53.13        34.55        33.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EY TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YJ 
       74.40        72.00        63.29        32.55        50.47        18.61 
TCGA-A2-A1FZ TCGA-A2-A25C TCGA-A2-A3KD TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RY 
       22.45        17.19        39.65        47.31        50.37        21.30 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A13D TCGA-A7-A3RF TCGA-A7-A4SE 
       26.96        21.14        21.90        31.73        13.41        21.17 
TCGA-A7-A5ZV TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A08X TCGA-A8-A095 TCGA-A8-A0A4 
       12.10        53.98         9.01        43.00        41.98        13.02 
TCGA-AC-A23E TCGA-AC-A2FB TCGA-AC-A3W7 TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XP 
       22.95        40.57        15.48         7.59         0.33         0.30 
TCGA-AO-A03M TCGA-AO-A0JB TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U2 TCGA-AR-A0U4 
       61.35        50.70        64.83        55.86        83.87       107.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24Q TCGA-AR-A2LE TCGA-B6-A0I9 TCGA-B6-A0IK 
       86.53        86.43       104.28       166.42        11.90        18.77 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-BH-A0AV TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0E1 
       68.45       212.25        59.84        77.75        46.39        15.68 
TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18J 
       14.30        63.32        23.08        50.79         5.59        20.12 
TCGA-BH-A18L TCGA-BH-A1EO TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FH 
       26.66        91.99        49.58        17.69        97.48        33.99 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HO 
       12.66        12.56        12.16        13.51        12.46        12.33 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A8HP TCGA-D8-A1JK TCGA-D8-A1X5 
       12.53        12.36        12.95        13.02        20.12        18.58 
TCGA-D8-A1X7 TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A27R 
       16.73        12.39        15.22        21.83        14.50        10.09 
TCGA-D8-A3Z5 TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A1B6 TCGA-E2-A1LB TCGA-E2-A1LL 
       33.37        31.96        69.34        28.50        75.81        43.04 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A22E 
       35.24        25.84         9.86        11.15        40.24        41.72 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
        0.69         7.13        38.07        26.70        25.81        26.40 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6SC TCGA-GI-A2C8 
       29.85        40.41        52.73        17.52        31.30         7.40 
TCGA-GM-A3XG TCGA-LL-A5YL TCGA-LL-A6FR TCGA-OL-A5DA TCGA-OL-A5RZ TCGA-OL-A5S0 
       43.73        17.06        16.08        58.62        22.32        20.38 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-AA15 
       41.92        26.04        14.07        17.26 

$subtype6
TCGA-E2-A1L8 TCGA-A2-A0CX TCGA-A2-A0EO TCGA-A2-A0T1 TCGA-A2-A25F TCGA-A2-A4RX 
       73.64        56.81        80.28        17.13        10.59        24.39 
TCGA-A7-A0DA TCGA-A7-A26G TCGA-A8-A075 TCGA-A8-A0A7 TCGA-AN-A0AM TCGA-AN-A0XW 
       35.67        23.74        17.03         0.99         0.16         5.59 
TCGA-AO-A03U TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
       58.95        76.77        55.33       106.78       102.31        82.68 
TCGA-AR-A0TS TCGA-AR-A1AT TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A251 TCGA-AR-A254 
       84.10        41.82         2.76        97.84        99.62        85.64 
TCGA-B6-A0WX TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0EB TCGA-BH-A18F 
       21.01        77.95        74.14        41.75        24.49        32.91 
TCGA-BH-A18G TCGA-BH-A18P TCGA-BH-A1EV TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A2L8 
        4.90        30.28        12.00        72.07        57.83        20.12 
TCGA-C8-A12O TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-D8-A142 TCGA-D8-A1J8 
       12.66        12.59        12.59        12.49        13.97        14.17 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XW 
       18.15        53.00        20.09        17.69        16.41        43.04 
TCGA-D8-A1XY TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N TCGA-E2-A15H 
       16.54        14.24        13.05        13.48        17.06        12.92 
TCGA-E2-A1B0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A227 
       53.62         2.56         6.12         6.58        47.64        32.05 
TCGA-E9-A22A TCGA-E9-A3QA TCGA-EW-A1OV TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GM-A2DB 
       39.09        30.18        25.94        55.00        17.49        79.10 
TCGA-JL-A3YW 
       11.84 

$subtype7
TCGA-A2-A0YG TCGA-A2-A3XV TCGA-A8-A08J TCGA-A8-A09W TCGA-A8-A09X TCGA-B6-A0IG 
       21.90        32.75        37.05         0.99        14.01       146.50 
TCGA-BH-A0B7 TCGA-BH-A1F2 TCGA-D8-A1XS TCGA-E2-A1LE 
       84.13        31.53        16.31        28.90 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.03     0.23     0.33     0.33     0.30     0.16     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  282.90   170.17    89.06   263.28   212.25   106.78   146.50 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  22.010   27.550   17.030   37.740   26.530   24.390   30.215 
[1] "0.0 - 282.9 (22.0)" "0.2 - 170.2 (27.6)" "0.3 - 89.1 (17.0)" 
[4] "0.3 - 263.3 (37.7)" "0.3 - 212.2 (26.5)" "0.2 - 106.8 (24.4)"
[7] "1.0 - 146.5 (30.2)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       6       11        0        3        80        52         0
  subtype2      17       22        1        0        73        63         1
  subtype3       3        5        0        0         8         5         0
  subtype4      22       18        1        1        52        58         1
  subtype5       9        2        2        0        55        21         0
  subtype6       5        6        0        0        27        12         0
  subtype7       0        0        0        0         1         2         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         21          3         14        7       0
  subtype2         38          6         10        4       3
  subtype3          4          2          0        0       1
  subtype4         34          4         12        3       1
  subtype5         23          6         10        3       1
  subtype6         14          0          3        0       0
  subtype7          0          2          4        1       0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           6       17        3       22        9        5        0
  STAGE IA         11       22        5       18        2        6        0
  STAGE IB          0        1        0        1        2        0        0
  STAGE II          3        0        0        1        0        0        0
  STAGE IIA        80       73        8       52       55       27        1
  STAGE IIB        52       63        5       58       21       12        2
  STAGE III         0        1        0        1        0        0        0
  STAGE IIIA       21       38        4       34       23       14        0
  STAGE IIIB        3        6        2        4        6        0        2
  STAGE IIIC       14       10        0       12       10        3        4
  STAGE IV          7        4        0        3        3        0        1
  STAGE X           0        3        1        1        1        0        0
[1] 12  7
[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  31 138  24   6
  subtype2  57 143  30   8
  subtype3  10  14   2   4
  subtype4  66 104  33   5
  subtype5  21  81  20  11
  subtype6  16  45   6   0
  subtype7   0   8   0   2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       31       57       10       66       21       16        0
  T2      138      143       14      104       81       45        8
  T3       24       30        2       33       20        6        0
  T4        6        8        4        5       11        0        2
[1] 4 7
[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 101  62  19  16
  subtype2 107  85  28  13
  subtype3  16   5   5   1
  subtype4  88  78  25  14
  subtype5  63  40  17  12
  subtype6  36  18  10   3
  subtype7   1   3   0   6
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0      101      107       16       88       63       36        1
  N1       62       85        5       78       40       18        3
  N2       19       28        5       25       17       10        0
  N3       16       13        1       14       12        3        6
[1] 4 7
[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 161   8
  subtype2 201   4
  subtype3  28   0
  subtype4 175   4
  subtype5 102   3
  subtype6  63   0
  subtype7   9   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  161    8
  subtype2  201    4
  subtype3   28    0
  subtype4  175    4
  subtype5  102    3
  subtype6   63    0
  subtype7    9    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0      161      201       28      175      102       63        9
  1        8        4        0        4        3        0        1
[1] 2 7
[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 197   2
  subtype2 234   5
  subtype3  30   0
  subtype4 206   2
  subtype5 133   0
  subtype6  67   0
  subtype7   9   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  197    2
  subtype2  234    5
  subtype3   30    0
  subtype4  206    2
  subtype5  133    0
  subtype6   67    0
  subtype7    9    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE      197      234       30      206      133       67        9
  MALE          2        5        0        2        0        0        1
[1] 2 7
[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  87  92
  subtype2 112 110
  subtype3   9  17
  subtype4  66 129
  subtype5  65  58
  subtype6  25  36
  subtype7   1   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   87   92
  subtype2  112  110
  subtype3    9   17
  subtype4   66  129
  subtype5   65   58
  subtype6   25   36
  subtype7    1    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        87      112        9       66       65       25        1
  YES       92      110       17      129       58       36        6
[1] 2 7
[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                           167
  subtype2                          0                           166
  subtype3                          0                            24
  subtype4                          0                           130
  subtype5                          1                            92
  subtype6                          0                            56
  subtype7                          0                             7
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             12                   4
  subtype2                             40                   0
  subtype3                              4                   0
  subtype4                             69                   1
  subtype5                             23                   0
  subtype6                              5                   1
  subtype7                              2                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     2                                3
  subtype2                     0                                9
  subtype3                     1                                1
  subtype4                     0                                5
  subtype5                     3                                4
  subtype6                     1                                1
  subtype7                     0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  2              9
  subtype2                  7             17
  subtype3                  0              0
  subtype4                  1              2
  subtype5                  4              6
  subtype6                  0              3
  subtype7                  0              1
D5V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         167      166       24      130       92
  INFILTRATING LOBULAR CARCINOMA         12       40        4       69       23
  MEDULLARY CARCINOMA                     4        0        0        1        0
  METAPLASTIC CARCINOMA                   2        0        1        0        3
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        9        1        5        4
  MUCINOUS CARCINOMA                      2        7        0        1        4
  OTHER, SPECIFY                          9       17        0        2        6
                                  clus
vv                                 subtype6 subtype7
  INFILTRATING CARCINOMA NOS              0        0
  INFILTRATING DUCTAL CARCINOMA          56        7
  INFILTRATING LOBULAR CARCINOMA          5        2
  MEDULLARY CARCINOMA                     1        0
  METAPLASTIC CARCINOMA                   1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        0
  MUCINOUS CARCINOMA                      0        0
  OTHER, SPECIFY                          3        1
[1] 8 7
[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                                0    19                        57
  subtype2                                0    12                        26
  subtype3                                0     1                         4
  subtype4                                0    12                        18
  subtype5                                0    10                        23
  subtype6                                1     5                         8
  subtype7                                0     0                         1
          vv
clus       WHITE
  subtype1   112
  subtype2   184
  subtype3    19
  subtype4   168
  subtype5    89
  subtype6    51
  subtype7     6
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                  19       12        1       12       10
  BLACK OR AFRICAN AMERICAN              57       26        4       18       23
  WHITE                                 112      184       19      168       89
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        1        0
  ASIAN                                   5        0
  BLACK OR AFRICAN AMERICAN               8        1
  WHITE                                  51        6
[1] 4 7
[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   6 170
  subtype2   8 196
  subtype3   1  22
  subtype4  10 164
  subtype5   2 110
  subtype6   1  61
  subtype7   0   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  170
  subtype2    8  196
  subtype3    1   22
  subtype4   10  164
  subtype5    2  110
  subtype6    1   61
  subtype7    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        8        1       10        2        1
  NOT HISPANIC OR LATINO      170      196       22      164      110       61
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        7
[1] 2 7
[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 185  37
  subtype2 342  54
  subtype3 225  31
subtype1 subtype2 subtype3 
     222      396      256 
subtype1 subtype2 subtype3 
      37       54       31 
$subtype1
TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A09I TCGA-AC-A62X TCGA-AQ-A54N 
       24.26        21.73        22.32        45.07        13.71         2.56 
TCGA-AR-A2LR TCGA-E2-A158 TCGA-LL-A5YP TCGA-3C-AALI TCGA-A1-A0SK TCGA-A1-A0SO 
       57.27        14.79        14.79       131.67        31.79        28.01 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0CX 
       18.02        73.84        87.25       101.98        24.79        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0ST 
       67.33        34.55        33.76        79.76        63.29        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG 
       50.43        17.52        17.13         8.38        18.21        21.90 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       18.61        31.73        10.59        91.07        29.98        32.75 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       50.37        24.39        35.31        35.67        31.73        20.19 
TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A8-A075 TCGA-A8-A07I TCGA-A8-A07O 
       23.74        14.50        12.10        17.03        14.01         9.99 
TCGA-A8-A07R TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 
        8.98        37.05         9.99        43.00        14.01         0.99 
TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
       73.05        14.66         1.71         7.46         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0G0 
        7.96         7.59         7.04         0.33         0.33         0.53 
TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JE TCGA-AO-A0JL 
        0.33        58.95        32.78        37.48        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        82.68        60.56        82.62 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0TX TCGA-AR-A0U0 
      140.55        98.33        84.10        23.31        64.83        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO 
      133.22       107.21       125.16       108.36       101.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 
       99.32        41.82        33.73       104.28       102.84        99.62 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0I6 TCGA-B6-A0I9 
       85.64        93.83        20.25        10.59        32.58        11.90 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX 
      233.62       140.88       212.25        89.46       282.90        21.01 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BW 
      245.10        59.84        39.55        84.13        51.68        77.95 
TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0EE TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18R 
       78.28         4.41        31.00         4.90        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F2 
        7.36        51.16        69.93        12.00        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       97.48       114.15        72.07        26.14        38.60        57.83 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Z TCGA-C8-A131 
       11.93        11.77        12.66        12.66        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HJ 
       12.59        12.59        12.92        12.46        10.92         0.16 
TCGA-C8-A1HK TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       12.03        12.36        12.95         0.03         9.76        14.43 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.88        13.97        14.17        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       16.50        12.03        53.00        20.12        20.09        19.40 
TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW 
       18.58        21.83        14.50        16.41        16.64        43.04 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N TCGA-E2-A14N TCGA-E2-A14P 
       16.04        13.05        13.48        17.06        47.15        40.96 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H 
       31.96        69.34        63.62        69.96        25.05        12.92 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK 
       76.57        53.62        28.50        75.81        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A3DX TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1ND 
       43.04        52.73        43.56        38.76        34.16        41.62 
TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL 
       40.73        20.12         0.69         1.94        30.18         0.79 
TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P8 TCGA-EW-A1PB 
       16.57        25.94        22.82        40.41         7.86        19.99 
TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB 
       55.00        17.49        15.22         7.40       109.87        79.10 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A441 TCGA-LL-A5YO 
       70.85        72.10        69.30        11.84        32.75        14.47 
TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66P TCGA-S3-AA15 
       16.08        58.52        36.36        22.32        14.07        17.26 

$subtype2
TCGA-5L-AAT1 TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A7-A0CD 
       48.36        63.12        36.13        88.60        19.56        38.30 
TCGA-A8-A06U TCGA-A8-A091 TCGA-A8-A09C TCGA-A8-A09E TCGA-AC-A3W5 TCGA-AC-A5XS 
       29.03        33.01         1.02        49.05        16.57        19.33 
TCGA-AO-A1KT TCGA-AQ-A54O TCGA-AR-A2LL TCGA-B6-A0I8 TCGA-BH-A0B6 TCGA-BH-A18H 
       17.79        32.91        66.15        24.62        81.63        21.44 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A15O TCGA-E2-A2P5 
       89.16         9.70        10.42        21.14        50.79        26.99 
TCGA-EW-A1J5 TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A740 
       15.68        85.35        13.22        29.23        25.05        14.50 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-4H-AAAK 
       18.87        13.94        52.96       108.07        47.61        11.44 
TCGA-5T-A9QA TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SQ TCGA-A2-A0CK TCGA-A2-A0CS 
        9.96        48.10        47.24        18.21       136.73        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CY TCGA-A2-A0D3 
       75.25         5.19        98.99       107.93        55.00        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T5 
       25.22        80.28        54.64        27.12        44.88        17.46 
TCGA-A2-A0YD TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B 
       25.28        21.67        17.36        60.72        20.25        42.44 
TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A4S0 TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB 
       18.15        39.65        23.21        35.47        30.61        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       29.79        25.15        10.59        13.41        14.70        14.93 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y 
       17.92        10.29        10.42        17.98        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 
        1.02         7.99         9.99        45.07        18.05        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08T TCGA-A8-A099 TCGA-A8-A09A 
       13.02         0.99        19.96       112.08         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-AC-A2FM TCGA-AC-A2QI 
       12.00        33.07         8.98         0.99        26.04        19.33 
TCGA-AC-A3TM TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A6IX 
       25.05        24.79        29.26        14.96        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        1.68         1.12         2.96         9.96         7.36         0.16 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY 
        0.33         6.44         5.65         7.00         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.30         0.33         0.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0JB 
       66.77        81.63        95.70        21.40        20.32        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B 
       50.86        72.00        26.24       108.72       102.31        98.27 
TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AO-A1KS 
       77.98        70.42        53.88        40.57        61.87        11.51 
TCGA-AQ-A1H2 TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U3 TCGA-AR-A1AP 
       15.62         5.26       109.02        98.93       134.14        93.90 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P 
       37.81        61.28        50.89       120.33        99.78         2.76 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QN 
      112.77        97.84        98.66        93.30        54.21        33.30 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RO 
      129.57       146.50        68.45        81.17        78.02       162.05 
TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-B6-A2IU TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ 
      102.77       129.70       170.17        85.87        49.94        74.14 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DS 
       41.75        89.06        81.73        38.01        13.91         2.56 
TCGA-BH-A0DT TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0H5 TCGA-BH-A0H9 
       79.00        14.30        44.81        24.49        53.26        41.00 
TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
       52.96         5.85         2.37        12.89        51.32        27.25 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S 
       24.95        42.35        32.91        37.74        30.28        66.05 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FG 
      113.82        82.85        42.28        25.08        33.17       122.83 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 
       63.35        45.63        53.98        28.14        83.31       130.16 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ 
       20.12        10.52        20.88         9.63         5.26        18.87 
TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       21.76        11.77        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
       12.16        12.49        12.33        11.34        11.28        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       12.95        12.33        20.25        15.45        16.87        24.56 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        15.78        18.15        18.90        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XS 
       15.22        14.73        19.92        17.69        55.30        16.31 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       12.99        15.16        16.54        15.32         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       17.42        48.03        16.41         1.61        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A109 
       12.26        16.18        12.66        25.22        34.42        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14Q TCGA-E2-A14W TCGA-E2-A14Z 
       40.41        37.51        28.44        38.24        32.02        18.51 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15D 
       23.24        19.43        21.04        23.87        23.34        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R 
       20.71        18.21        53.92         9.04        20.58        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1L6 
       14.07        51.39        33.01        37.25        70.36        54.18 
TCGA-E2-A1L7 TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       60.36         8.28        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       22.29        36.20        36.56        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1RB 
        9.86        34.95         2.56         6.12         3.02        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-A22A TCGA-E9-A22B TCGA-E9-A22D 
       34.45        32.05        42.25        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
       41.72        40.50        38.99         7.13        24.56        29.72 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP 
       38.07        32.91        23.90        23.84        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1J1 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 
       27.85        18.90        29.95        29.85        41.13        23.11 
TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A6SA TCGA-EW-A6SB 
        6.15        52.73        25.91        22.09        16.77        24.99 
TCGA-EW-A6SD TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A5PV 
       33.21        59.57        83.34       106.06       101.62        13.55 
TCGA-HN-A2OB TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YN 
       62.47         7.10        13.28        10.62        15.32        14.70 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       22.26         2.63         7.46        19.53        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX 
       27.91        22.39        31.99        58.62        34.92        28.87 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       17.36        28.21        19.73        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.16         0.26        18.48        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-XX-A899 TCGA-Z7-A8R6 
       13.84        17.39        17.03         3.81        15.35       107.05 

$subtype3
TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A8-A07E TCGA-A8-A084 
      107.70        31.36        23.80        11.28        19.99        15.06 
TCGA-A8-A09K TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AO-A0JI TCGA-AQ-A7U7 TCGA-AR-A1AM 
       29.98        19.79        14.53        50.24        19.20        98.33 
TCGA-AR-A5QM TCGA-BH-A0EA TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A572 
       73.35        32.58        16.47        73.64        50.07        39.72 
TCGA-EW-A1P3 TCGA-GM-A2DD TCGA-LL-A440 TCGA-OL-A5RU TCGA-W8-A86G TCGA-A1-A0SJ 
       52.96        75.02        24.95        40.08        11.41        13.68 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CZ 
      143.15        78.41        99.12        92.48       107.93        53.13 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
      118.45        74.40        72.00        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       24.72        49.84        20.52        18.90        20.75        32.55 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       50.47        49.48        19.33        48.46        23.77        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E 
       22.45        19.20        16.47        52.47        17.19       105.34 
TCGA-A2-A3KC TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S1 
       36.23        56.28        47.31         7.30        21.30        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A3J0 TCGA-A7-A4SC 
       21.14        21.90        34.29        37.45        10.29        14.66 
TCGA-A7-A4SE TCGA-A8-A06P TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07P 
       21.17        13.02        53.98         9.01        18.97        10.98 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A0A4 TCGA-AC-A23C 
       31.00        31.00        40.01        41.98        13.02        19.23 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.95        22.26        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AN-A041 
       60.92        16.31        22.19        14.99        15.48         0.23 
TCGA-AN-A049 TCGA-AN-A0FS TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A0J5 
        0.62         6.90         0.33        12.33        80.28        26.04 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A1KO 
       22.36        53.03        65.10        62.04        71.80        20.45 
TCGA-AO-A1KP TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       97.08       130.09        32.52        75.22        55.86       107.24 
TCGA-AR-A0U2 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       83.87       103.86        97.68        94.29        86.53        86.43 
TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       94.22       118.59       105.27       105.30        50.96        98.76 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       89.00        71.05       166.42        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0IK TCGA-B6-A0IO 
       39.39        40.54        38.96       143.38        18.77       165.76 
TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      263.28       140.28       169.51        62.93        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC 
       81.44        37.74        39.16        70.22        37.22        32.02 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       43.53        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DI 
       76.60        77.75        46.39        90.97        67.10        29.98 
TCGA-BH-A0DP TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EI 
       15.65        67.86        15.68         9.63        81.83        63.32 
TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A0HY 
       30.35        24.56        23.08        16.96        13.61        50.79 
TCGA-BH-A0RX TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18U TCGA-BH-A1EO 
        5.59        20.12        26.66        72.56        51.39        91.99 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH 
       55.69        49.58        17.69       120.62        74.73        33.99 
TCGA-BH-A1FL TCGA-BH-A28Q TCGA-BH-A42U TCGA-C8-A12N TCGA-C8-A12U TCGA-C8-A26W 
       55.00        36.79       110.60        11.77        12.66        12.53 
TCGA-C8-A274 TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-D8-A145 TCGA-D8-A1X7 TCGA-D8-A1XA 
       16.70        33.99        13.02        13.48        16.73        27.58 
TCGA-D8-A1XR TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27V 
       15.85        15.52        14.24        13.45        14.43        12.53 
TCGA-D8-A3Z5 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       33.37        27.52        40.11        44.68        33.17        75.98 
TCGA-E2-A14V TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15P 
       34.26        22.82        21.63        55.63        11.05        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E9-A1NH TCGA-E9-A1QZ 
       87.22        32.35         3.88        11.08        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RH TCGA-E9-A229 
       28.27        11.15        48.23        45.01        46.59        37.74 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IZ 
       12.33         9.47        30.44        26.70        39.72        18.21 
TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE 
       13.25        39.78        29.82        18.90        13.94        10.52 
TCGA-EW-A1PG TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SC TCGA-GM-A2DI TCGA-GM-A2DK 
       34.55        17.52        23.51        31.30        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX 
      115.69        38.20        43.73        66.38        72.03        18.12 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-OL-A5RY TCGA-OL-A5S0 
        2.60        11.57        21.24        17.06        24.72        20.38 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66N 
       23.47        65.62        41.92        26.04 

subtype1 subtype2 subtype3 
    0.03     0.16     0.23 
subtype1 subtype2 subtype3 
  282.90   170.17   263.28 
subtype1 subtype2 subtype3 
  28.255   24.590   34.275 
[1] "0.0 - 282.9 (28.3)" "0.2 - 170.2 (24.6)" "0.2 - 263.3 (34.3)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       9       13        0        1        98        50         1
  subtype2      29       33        1        2       118        97         1
  subtype3      24       18        3        1        80        66         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         26          4         15        4       0
  subtype2         66         14         24       10       5
  subtype3         42          5         14        4       1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9       29       24
  STAGE IA         13       33       18
  STAGE IB          0        1        3
  STAGE II          1        2        1
  STAGE IIA        98      118       80
  STAGE IIB        50       97       66
  STAGE III         1        1        0
  STAGE IIIA       26       66       42
  STAGE IIIB        4       14        5
  STAGE IIIC       15       24       14
  STAGE IV          4       10        4
  STAGE X           0        5        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  41 150  25   9
  subtype2  89 240  53  18
  subtype3  71 143  37   9
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       41       89       71
  T2      150      240      143
  T3       25       53       37
  T4        9       18        9
[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 114  70  20  18
  subtype2 184 126  52  29
  subtype3 114  95  32  18
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      114      184      114
  N1       70      126       95
  N2       20       52       32
  N3       18       29       18
[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"
D6V6, binary
          cls
clus         0   1
  subtype1 197   5
  subtype2 330  10
  subtype3 212   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  197    5
  subtype2  330   10
  subtype3  212    5
   clus
vv  subtype1 subtype2 subtype3
  0      197      330      212
  1        5       10        5
[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"
D6V7, binary
          cls
clus         0   1
  subtype1 225   0
  subtype2 393   8
  subtype3 258   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  225    0
  subtype2  393    8
  subtype3  258    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      225      393      258
  MALE          0        8        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"
D6V8, binary
          cls
clus         0   1
  subtype1  92 109
  subtype2 177 195
  subtype3  96 144
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  109
  subtype2  177  195
  subtype3   96  144
     clus
vv    subtype1 subtype2 subtype3
  NO        92      177       96
  YES      109      195      144
[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                           199
  subtype2                          0                           285
  subtype3                          0                           158
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              7                   3
  subtype2                             60                   2
  subtype3                             88                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     4                                0
  subtype2                     1                               17
  subtype3                     2                                6
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  0             11
  subtype2                 13             23
  subtype3                  1              4
D6V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         199      285      158
  INFILTRATING LOBULAR CARCINOMA          7       60       88
  MEDULLARY CARCINOMA                     3        2        1
  METAPLASTIC CARCINOMA                   4        1        2
  MIXED HISTOLOGY (PLEASE SPECIFY)        0       17        6
  MUCINOUS CARCINOMA                      0       13        1
  OTHER, SPECIFY                         11       23        4
[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"
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    21                        49
  subtype2                                0    26                        65
  subtype3                                0    12                        23
          vv
clus       WHITE
  subtype1   140
  subtype2   283
  subtype3   206
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  21       26       12
  BLACK OR AFRICAN AMERICAN              49       65       23
  WHITE                                 140      283      206
[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"
D6V12, binary
          cls
clus         0   1
  subtype1   5 192
  subtype2  12 336
  subtype3  11 202
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  192
  subtype2   12  336
  subtype3   11  202
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5       12       11
  NOT HISPANIC OR LATINO      192      336      202
[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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 227  35
  subtype2 128  39
  subtype3 134  13
  subtype4 201  24
  subtype5 178  29
  subtype6  45   6
  subtype7  15   5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     262      167      147      225      207       51       20 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      35       39       13       24       29        6        5 
$subtype1
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A8-A08F TCGA-A8-A091 
       63.12        36.13        19.56        38.30        33.01        33.01 
TCGA-A8-A09E TCGA-A8-A09K TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54O TCGA-BH-A1F5 
       49.05        29.98        50.24        17.79        32.91        89.16 
TCGA-E2-A15O TCGA-GM-A2DO TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AAAU 
       50.79        85.35        18.87        13.94        52.96       133.05 
TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A0CT 
       48.46         9.96        13.68        18.21       121.94        75.25 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU 
        5.19       107.93        25.22        74.40        35.05        34.29 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.84        20.52        21.67        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A4RW TCGA-A2-A4S0 
       60.72        42.44        17.19       105.34         7.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IZ 
       21.90        30.61        37.45        25.15        20.61        10.59 
TCGA-A7-A3RF TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A06Z 
       13.41        13.74        17.92        13.02        31.00         1.02 
TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        9.01        32.05        10.98         9.99        45.07        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A09D TCGA-A8-A09M 
       36.95        13.02        19.96        12.00        50.04        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A5XU 
       25.02         8.98        38.04        99.35        26.04        14.96 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A7VB TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A049 
       11.44        18.67         8.22         0.33         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FW TCGA-AN-A0FY 
        2.96         7.36         6.44         5.65         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03V 
        0.33         0.33        61.35        95.70        69.83        44.42 
TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A126 TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ 
       21.40        20.32       108.72        40.57        97.08        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV 
       11.51        24.79        15.62        98.33       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AU 
       98.93        55.86       107.24        83.87       134.14        94.29 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A252 
      160.90        94.22       112.77       105.30        98.66        93.30 
TCGA-AR-A2LK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL 
       54.21       127.33        84.59       165.76        68.45        81.17 
TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X4 TCGA-B6-A0X5 
       78.02       188.68        79.46        18.35        28.27        68.94 
TCGA-B6-A1KC TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0B8 TCGA-BH-A0BV TCGA-BH-A0C7 
       43.59        62.93        39.16        51.58        49.94        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E2 TCGA-BH-A0E7 
       81.73        77.98        38.01         3.22        14.30        44.81 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       63.32        10.78        15.16        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HL TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L 
       52.96        26.50         2.37        51.32        27.25        26.66 
TCGA-BH-A18N TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EW TCGA-BH-A1F8 TCGA-BH-A1FG 
       37.74        91.99       113.82        55.69        25.08       122.83 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A42T TCGA-BH-A6R8 TCGA-C8-A12M 
       45.63        53.98        83.31        10.52         9.63        11.77 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HG TCGA-C8-A1HN 
       12.66        12.66        12.66        48.53        11.34        12.95 
TCGA-C8-A1HO TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HQ 
       12.33        15.45        16.87        24.56        12.95        12.49 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X5 
       56.81        13.25        15.78        18.97        13.32        18.58 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XZ 
       23.90        27.58        17.16        15.22        14.73        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27R TCGA-D8-A27W 
       15.52         9.93        14.14        13.45        10.09        12.26 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S 
       43.00        83.54        46.59        40.41        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15R 
       75.98        32.02        21.04        23.34        21.63        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L7 
       14.07        51.39        77.65        70.36        33.73        60.36 
TCGA-E2-A1LA TCGA-E2-A56Z TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1NA 
       24.59         8.28        34.29        34.82        36.82        36.56 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RG 
       34.95         6.12        11.15        48.23        46.65        21.27 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 
       42.25        39.09        38.37        41.03        38.99        12.33 
TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1IZ TCGA-EW-A1J1 
       29.72        23.90        23.84        25.81        18.21        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1PA 
       28.77        29.95        29.85        40.41        41.13        18.90 
TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A423 TCGA-EW-A6SA TCGA-EW-A6SC 
       13.94        52.73        22.09        17.52        16.77        31.30 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-OL-A5D8 
       83.34        86.96        15.32        12.36        17.49        31.99 
TCGA-OL-A66H TCGA-OL-A66O TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-A6ZF 
       26.70        17.36        40.11        47.01         0.16        18.81 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-UL-AAZ6 TCGA-Z7-A8R6 
       21.07        13.84        17.03       107.05 

$subtype2
TCGA-A7-A26F TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A07E TCGA-A8-A084 TCGA-A8-A08S 
       24.26        22.32        29.03        19.99        15.06        33.01 
TCGA-A8-A09I TCGA-AC-A3W5 TCGA-AQ-A0Y5 TCGA-B6-A0I8 TCGA-C8-A1HL TCGA-GM-A2DD 
       45.07        16.57         5.65        24.62        10.42        75.02 
TCGA-LL-A740 TCGA-3C-AALI TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W 
       14.50       131.67        20.88         7.96        39.32       101.98 
TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SV 
       55.43        56.81        34.55        31.82        63.29        27.12 
TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A2-A3XV TCGA-A2-A3XZ TCGA-A7-A56D 
       44.88        17.13        21.90        32.75        50.37        14.73 
TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
       10.42         1.02        17.98        17.03        53.98        43.00 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A092 
       18.97        14.01        37.05         9.99        31.00        30.97 
TCGA-A8-A097 TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A23C 
       12.00         1.02         0.99        14.01         0.99        19.23 
TCGA-AC-A23H TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0FT 
        5.72         6.48        16.80         1.78         9.96         7.04 
TCGA-AN-A0FV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0JA 
        0.33         5.59        80.28        66.77        32.78        21.53 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX 
       72.00        76.77        71.80        82.68       130.09        64.83 
TCGA-AR-A1AT TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A254 TCGA-B6-A0I9 TCGA-B6-A0IG 
       41.82       102.84        89.00        85.64        11.90       146.50 
TCGA-B6-A0IK TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A1KN TCGA-BH-A0AW TCGA-BH-A0B7 
       18.77       212.25       100.70       139.17        20.45        84.13 
TCGA-BH-A0BA TCGA-BH-A0BR TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DG 
       37.22        76.60        74.14        41.75        46.39        67.10 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0HY TCGA-BH-A0W7 
       70.88        16.27        31.00        30.35        50.79        44.81 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18U TCGA-BH-A1EN 
       20.12        90.84        30.28        37.55        51.39        69.93 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1FU TCGA-BH-A202 
       12.00        49.58        17.69        31.53        55.50        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       38.60        57.83        11.93        12.66        11.77        12.66 
TCGA-C8-A12Z TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK 
       12.56        12.92        12.46        12.49        10.92        12.03 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 
       12.36        12.95        16.70         0.03         9.76        33.99 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF 
       13.02        20.88        14.17        17.49        16.50        12.03 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1XJ TCGA-D8-A1XT 
       53.00        20.09        20.12        20.38        21.83        16.64 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V 
       12.99        16.54        17.06        40.11        40.96        34.26 
TCGA-E2-A152 TCGA-E2-A1B0 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E9-A1N6 TCGA-E9-A1NF 
       69.96        53.62        75.81        28.90        22.29        35.24 
TCGA-E9-A1NG TCGA-E9-A1R5 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22E 
       25.84         3.02         6.58        46.59        34.45        41.72 
TCGA-E9-A248 TCGA-EW-A2FR TCGA-EW-A6S9 TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2DB 
        1.94        55.00        15.22        33.21         7.40        79.10 
TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO TCGA-OL-A5D6 
       72.10        11.84        10.62        17.06        14.47        36.30 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66P TCGA-UU-A93S TCGA-WT-AB44 
       24.72        22.32        14.07         3.81        29.03 

$subtype3
TCGA-5L-AAT0 TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A426 TCGA-A7-A5ZX TCGA-AR-A1AM 
       48.56       107.70        31.36        11.97        11.05        98.33 
TCGA-BH-A0DO TCGA-LD-A74U TCGA-LL-A440 TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALK 
       54.05        13.22        24.95        11.41       108.07        47.61 
TCGA-4H-AAAK TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A2-A0CP 
       11.44        14.37        43.43        48.10        47.24        92.48 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES TCGA-A2-A0EW 
      107.93        98.99        53.13        80.28        72.00        61.94 
TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0T7 TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G0 
       24.72        54.64        20.75        19.33        48.46        20.25 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A7-A0CG 
       16.47        52.47        36.23        39.65        21.30        34.29 
TCGA-A7-A13H TCGA-A7-A5ZW TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A0A4 TCGA-A8-A0A6 
       29.56        10.72        31.00         9.99        13.02        21.04 
TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A3OD 
       73.91        40.57        90.71        60.92        87.12        14.83 
TCGA-AC-A3QP TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AN-A0FS TCGA-AO-A03R TCGA-AO-A0JG 
       22.19        15.48        23.24         6.90        68.75        26.24 
TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KO TCGA-AR-A1AK 
      102.31        77.98        70.42        53.88        20.45       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W 
       97.68        86.07       120.33       118.59       105.27        50.96 
TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QP 
       71.05        20.25        63.62        39.39        40.54        38.96 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-B6-A0X7 
       65.52       112.37       140.28       169.51       113.79        58.55 
TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       63.09        37.74        32.02        21.70        61.68        72.23 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DV TCGA-BH-A0E9 TCGA-BH-A0H3 TCGA-BH-A0HF 
       29.98        13.91        67.86        81.83        63.39        23.90 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18M TCGA-BH-A1FB 
       13.61        36.85        24.95        42.35        72.56       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V 
       74.73        33.99        28.14        36.82       110.60        20.88 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A8HR TCGA-D8-A145 
       18.87        21.76        12.59        11.28        13.41        13.48 
TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1XB TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27P 
       55.50        14.01        18.15        14.43        16.41         1.61 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14U 
       12.53        33.37        18.51        21.67        38.24        43.33 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1IJ 
       22.82        20.71        12.92        19.56        87.22        28.44 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1RI TCGA-EW-A1IW 
       60.99        54.18        36.20        35.77        47.64        12.20 
TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV TCGA-GM-A3XG 
       13.25        39.78        14.43        34.55        25.91        43.73 
TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LL-A73Z TCGA-MS-A51U TCGA-OL-A5RV TCGA-OL-A5RX 
       13.55        62.47         7.46        22.39        34.92        28.87 
TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-S3-AA14 
       19.73         0.26        17.39 

$subtype4
TCGA-5L-AAT1 TCGA-A2-A0CQ TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A8-A06T 
       48.36        88.60        23.61        23.80        11.28        53.06 
TCGA-A8-A093 TCGA-A8-A09C TCGA-AR-A2LL TCGA-BH-A0EA TCGA-BH-A8FY TCGA-D8-A146 
       17.95         1.02        66.15        32.58         9.70        21.14 
TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-E2-A572 TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-LL-A442 
       73.64        26.99        39.72        15.68        52.96        29.23 
TCGA-LL-A50Y TCGA-OL-A5RU TCGA-A1-A0SG TCGA-A2-A04N TCGA-A2-A0CS TCGA-A2-A0D3 
       25.05        40.08        14.27       143.15        77.19        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0SY TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
      101.72       134.40        44.28        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A4S2 TCGA-A7-A0CH TCGA-A7-A0DB 
       25.28        50.47        49.48        21.14        35.47        33.11 
TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08C 
       13.02        26.01        18.97         7.99         0.99        28.96 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09T 
      112.08        40.01        41.98         9.99        12.00        19.04 
TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E 
       15.02        12.00        19.04        27.02        17.03        22.95 
TCGA-AC-A2B8 TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QQ TCGA-AC-A3TM 
       22.26        19.33        32.45        16.31        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A046 
       14.99        24.79        17.42         1.68         0.33         0.33 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        7.00         7.17        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A0J8 TCGA-AO-A0JF TCGA-AO-A125 TCGA-AO-A12B TCGA-AQ-A1H3 
        5.33        22.36        65.10       113.62        98.27        32.52 
TCGA-AR-A0TR TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24N 
        5.26        93.90        37.81        61.28        50.89        99.78 
TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24X TCGA-AR-A2LE TCGA-B6-A0I5 TCGA-B6-A0IA 
        2.76        97.84        98.76       166.42       281.29       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO 
      129.57        50.70       129.07       234.28       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0WS TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A1KI TCGA-B6-A2IU 
      102.77        97.48       206.86       129.70        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B0 TCGA-BH-A0B5 
       85.35        68.12       103.63        71.15        81.44        70.22 
TCGA-BH-A0BD TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DP TCGA-BH-A0DS 
       18.21        74.14        85.87        77.75        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0HO 
       79.00        15.68        24.49        20.38        16.96         2.50 
TCGA-BH-A0HU TCGA-BH-A0W3 TCGA-BH-A18I TCGA-BH-A18S TCGA-BH-A1ET TCGA-BH-A1EU 
       12.89        23.93        35.93        66.05        82.85        42.28 
TCGA-BH-A1FD TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A5J0 
       33.17        63.35        55.00        36.79        20.12        23.51 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26W TCGA-D8-A141 
        9.44        11.77        12.33        20.25        12.53        20.58 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X6 TCGA-D8-A1X7 
       18.15        18.90        21.01        12.20        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       25.74        12.39        17.69        55.30        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27T TCGA-D8-A73U TCGA-D8-A73W 
       15.16        17.42        48.03        13.08        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A153 
       25.22        34.42        37.51        28.44        28.87        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       19.43        23.87        17.29        18.21        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IK 
        9.04        20.58        33.01        37.25        37.41        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A2P6 TCGA-E2-A3DX 
        3.88        22.19        11.08        19.66        34.55        43.56 
TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1RA 
       30.61        32.88        18.94         9.86         2.56        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22H 
       32.09        40.24         1.12        32.05        37.74        40.50 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-E9-A6HE 
        7.13        24.56        38.07        30.44        26.40        27.85 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PE 
       39.72         8.48        16.57        23.11        18.48        10.52 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XN 
       23.51        59.57       106.06       101.62        38.20        66.38 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A6FP 
       18.12        11.57        21.24        13.28        14.70        22.26 
TCGA-LL-A6FQ TCGA-OL-A5DA TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DD 
        2.63        58.62        41.92        42.77        26.04        64.21 
TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-V7-A7HQ 
       86.96        18.48        66.84 

$subtype5
TCGA-A1-A0SP TCGA-A7-A26I TCGA-AC-A62X TCGA-AQ-A54N TCGA-AR-A1AR TCGA-AR-A2LR 
       19.20        21.73        13.71         2.56        17.23        57.27 
TCGA-E2-A158 TCGA-E2-A1LG TCGA-LL-A5YP TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO 
       14.79        50.07        14.79         8.52        31.79        28.01 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY 
       18.02        78.41        73.84        87.25        24.79        55.00 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 
       67.33        33.76        99.19        50.43        17.52         8.38 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS 
       18.21        18.61        31.73        19.20        10.59        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       91.07        29.98        56.28        47.31        35.93        50.83 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       24.39        26.96        35.31        35.67        31.73        20.19 
TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       23.74        11.34        10.29        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-A08B TCGA-A8-A08R TCGA-A8-A08X TCGA-AC-A2BK TCGA-AC-A2QH 
       24.99        38.01         0.99        43.00        73.05        33.04 
TCGA-AC-A2QJ TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A04D 
       14.66        13.58         0.03         1.12         1.32         1.71 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        7.46         0.16         0.33         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A03U 
        7.59         0.33         0.53         0.33         0.33        58.95 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 
       52.18        37.48        50.70        55.33       115.27       106.78 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS 
      108.03        60.56        82.62        26.93       140.55        84.10 
TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       23.31        65.36       107.21       125.16       108.36       101.00 
TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ 
       99.32        33.73       104.28        99.62        93.83        10.59 
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-A0X1 TCGA-B6-A1KF TCGA-B6-A3ZX 
       89.46       282.90        21.01       245.10       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 
        7.07        74.99        18.84        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-A18Q TCGA-BH-A18T TCGA-BH-A18V 
        5.59        23.05         4.90        55.63         7.36        51.16 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A5IZ TCGA-BH-A6R9 
       25.81        97.48       114.15        72.07        18.64         5.26 
TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B 
       12.66        12.16        13.51        12.59         0.16        14.43 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK 
       13.97        14.17        19.20        20.09        19.40        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N 
       16.41        43.04        16.04        13.05        13.48        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A1AZ 
       38.60        31.96        69.34        63.62        25.05        76.57 
TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.50        33.70       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC 
       52.73        34.92        38.76        17.69        34.16        39.55 
TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL 
       41.62        40.73        20.12         0.69        30.18         0.79 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       22.82        29.82        30.08         7.86        19.99         6.15 
TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL 
       19.96        17.49        24.99       109.87        70.85        69.30 
TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 
        2.60        32.75        16.08        15.68        19.59        58.52 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ 
       36.36        20.38        23.47        28.21         8.91         9.93 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       20.68        19.27        17.26 

$subtype6
TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AR-A5QM TCGA-E2-A1BC TCGA-A2-A0CK TCGA-A2-A0CO 
       19.79        19.33        73.35        16.47       136.73       114.81 
TCGA-A2-A0EP TCGA-A2-A1FZ TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SC TCGA-A8-A07J 
      118.45        22.45        14.70        14.93        14.66        12.00 
TCGA-AC-A2FE TCGA-AC-A2FO TCGA-AC-A4ZE TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OS 
       86.66        74.14        29.26        12.26        20.19         2.30 
TCGA-AN-A0XL TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JJ TCGA-AR-A1AN TCGA-AR-A2LJ 
        5.36        26.04        53.03        62.04        96.00        86.53 
TCGA-AR-A2LN TCGA-AR-A5QN TCGA-BH-A0AY TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0HK 
       38.17        33.30        25.55        75.48        89.06         5.85 
TCGA-BH-A18F TCGA-D8-A1JU TCGA-E2-A108 TCGA-E2-A15M TCGA-E2-A1B5 TCGA-E9-A1QZ 
       32.91        14.70        27.52        11.05        32.35        24.82 
TCGA-E9-A1R0 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A5FK TCGA-EW-A3E8 TCGA-GM-A2DA 
       28.27         9.47        32.91        26.70        34.03       216.76 
TCGA-GM-A2DL TCGA-GM-A3NW TCGA-GM-A4E0 TCGA-LD-A7W5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
      115.69       110.50        72.03         7.10        27.91         2.10 
TCGA-OL-A66J TCGA-XX-A899 TCGA-XX-A89A 
       65.62        15.35        16.04 

$subtype7
TCGA-AQ-A7U7 TCGA-BH-A0B6 TCGA-BH-A18H TCGA-A2-A0CL TCGA-A2-A0EQ TCGA-A2-A25D 
       19.20        81.63        21.44        99.12        79.76        18.15 
TCGA-AO-A03O TCGA-AO-A0JC TCGA-AR-A1AW TCGA-AR-A1AX TCGA-BH-A0BF TCGA-BH-A0H5 
       81.63        50.86        86.53        86.43        43.53        53.26 
TCGA-BH-A209 TCGA-C8-A1HM TCGA-D8-A1XL TCGA-D8-A1Y2 TCGA-E2-A14Z TCGA-EW-A1OV 
      130.16        12.33        19.92        14.24        18.51        25.94 
TCGA-GM-A2DI TCGA-LL-A7SZ 
       85.15        19.53 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.16     0.03     0.26     0.30     0.03     2.10    12.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  188.68   212.25   169.51   281.29   282.90   216.76   130.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  29.245   24.260   36.200   25.740   26.960   27.910   47.195 
[1] "0.2 - 188.7 (29.2)"  "0.0 - 212.2 (24.3)"  "0.3 - 169.5 (36.2)" 
[4] "0.3 - 281.3 (25.7)"  "0.0 - 282.9 (27.0)"  "2.1 - 216.8 (27.9)" 
[7] "12.3 - 130.2 (47.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      18       16        4        1        81        73         1
  subtype2      10       12        0        1        54        38         0
  subtype3      12       14        1        1        31        40         1
  subtype4      25       24        1        1        77        43         0
  subtype5      14       15        0        1        93        47         0
  subtype6       5        3        0        1        16        11         0
  subtype7       6        1        0        0         6         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         44         12         10        3       4
  subtype2         28          6         12        6       2
  subtype3         25          0         16        3       2
  subtype4         29          5         10        4       5
  subtype5         22          4          7        3       1
  subtype6          6          0          9        1       0
  subtype7          2          0          1        0       0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          18       10       12       25       14        5        6
  STAGE IA         16       12       14       24       15        3        1
  STAGE IB          4        0        1        1        0        0        0
  STAGE II          1        1        1        1        1        1        0
  STAGE IIA        81       54       31       77       93       16        6
  STAGE IIB        73       38       40       43       47       11        4
  STAGE III         1        0        1        0        0        0        0
  STAGE IIIA       44       28       25       29       22        6        2
  STAGE IIIB       12        6        0        5        4        0        0
  STAGE IIIC       10       12       16       10        7        9        1
  STAGE IV          3        6        3        4        3        1        0
  STAGE X           4        2        2        5        1        0        0
[1] 12  7
[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  61 164  27  13
  subtype2  38 106  17  10
  subtype3  44  72  31   0
  subtype4  78 114  26   9
  subtype5  41 137  23   7
  subtype6  10  28  13   1
  subtype7   7  12   1   0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       61       38       44       78       41       10        7
  T2      164      106       72      114      137       28       12
  T3       27       17       31       26       23       13        1
  T4       13       10        0        9        7        1        0
[1] 4 7
[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 106 105  36  11
  subtype2  65  58  27  16
  subtype3  56  56  14  18
  subtype4 118  72  20  14
  subtype5 129  54  18   8
  subtype6  28  12   3   9
  subtype7  13   4   2   1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0      106       65       56      118      129       28       13
  N1      105       58       56       72       54       12        4
  N2       36       27       14       20       18        3        2
  N3       11       16       18       14        8        9        1
[1] 4 7
[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 225   4
  subtype2 144   6
  subtype3 119   3
  subtype4 186   4
  subtype5 178   4
  subtype6  35   1
  subtype7  16   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  225    4
  subtype2  144    6
  subtype3  119    3
  subtype4  186    4
  subtype5  178    4
  subtype6   35    1
  subtype7   16    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0      225      144      119      186      178       35       16
  1        4        6        3        4        4        1        0
[1] 2 7
[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 258   9
  subtype2 170   1
  subtype3 147   0
  subtype4 225   2
  subtype5 209   0
  subtype6  52   0
  subtype7  20   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  258    9
  subtype2  170    1
  subtype3  147    0
  subtype4  225    2
  subtype5  209    0
  subtype6   52    0
  subtype7   20    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE      258      170      147      225      209       52       20
  MALE          9        1        0        2        0        0        0
[1] 2 7
[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 112 134
  subtype2  72  74
  subtype3  59  80
  subtype4  95 116
  subtype5  81 107
  subtype6  19  30
  subtype7   7  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  112  134
  subtype2   72   74
  subtype3   59   80
  subtype4   95  116
  subtype5   81  107
  subtype6   19   30
  subtype7    7   12
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO       112       72       59       95       81       19        7
  YES      134       74       80      116      107       30       12
[1] 2 7
[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                           215
  subtype2                          0                           152
  subtype3                          0                            67
  subtype4                          0                           136
  subtype5                          1                           177
  subtype6                          0                            18
  subtype7                          0                            17
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             26                   0
  subtype2                             12                   0
  subtype3                             65                   0
  subtype4                             64                   0
  subtype5                              2                   5
  subtype6                             32                   0
  subtype7                              2                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                6
  subtype2                     1                                2
  subtype3                     0                                9
  subtype4                     0                                9
  subtype5                     8                                2
  subtype6                     0                                1
  subtype7                     0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  9             11
  subtype2                  0              4
  subtype3                  1              5
  subtype4                  4             14
  subtype5                  3             10
  subtype6                  0              1
  subtype7                  0              0
D7V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         215      152       67      136      177
  INFILTRATING LOBULAR CARCINOMA         26       12       65       64        2
  MEDULLARY CARCINOMA                     0        0        0        0        5
  METAPLASTIC CARCINOMA                   0        1        0        0        8
  MIXED HISTOLOGY (PLEASE SPECIFY)        6        2        9        9        2
  MUCINOUS CARCINOMA                      9        0        1        4        3
  OTHER, SPECIFY                         11        4        5       14       10
                                  clus
vv                                 subtype6 subtype7
  INFILTRATING CARCINOMA NOS              0        0
  INFILTRATING DUCTAL CARCINOMA          18       17
  INFILTRATING LOBULAR CARCINOMA         32        2
  MEDULLARY CARCINOMA                     0        1
  METAPLASTIC CARCINOMA                   0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        0
  MUCINOUS CARCINOMA                      0        0
  OTHER, SPECIFY                          1        0
[1] 8 7
[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    16                        47
  subtype2                                1    21                        24
  subtype3                                0     6                        13
  subtype4                                0     9                        23
  subtype5                                0     8                        69
  subtype6                                0     0                         2
  subtype7                                0     1                         5
          vv
clus       WHITE
  subtype1   177
  subtype2    99
  subtype3   123
  subtype4   172
  subtype5   122
  subtype6    46
  subtype7    14
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                  16       21        6        9        8
  BLACK OR AFRICAN AMERICAN              47       24       13       23       69
  WHITE                                 177       99      123      172      122
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               2        5
  WHITE                                  46       14
[1] 4 7
[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   9 211
  subtype2   2 133
  subtype3   7 120
  subtype4  12 176
  subtype5   6 178
  subtype6   2  43
  subtype7   1  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  211
  subtype2    2  133
  subtype3    7  120
  subtype4   12  176
  subtype5    6  178
  subtype6    2   43
  subtype7    1   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            9        2        7       12        6        2
  NOT HISPANIC OR LATINO      211      133      120      176      178       43
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       19
[1] 2 7
[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 247  41
  subtype2 127  36
  subtype3  82   9
  subtype4 267  26
  subtype5 159  27
  subtype6  46  12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     288      163       91      293      186       58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      41       36        9       26       27       12 
$subtype1
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A7-A13G TCGA-A7-A2KD 
       63.12        88.60        19.56        38.30        23.61        22.32 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-A8-A09E 
       53.06        29.03        33.01        17.95         1.02        49.05 
TCGA-A8-A09K TCGA-AO-A0JI TCGA-AO-A1KT TCGA-AQ-A54O TCGA-AR-A2LL TCGA-BH-A1F5 
       29.98        50.24        17.79        32.91        66.15        89.16 
TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A15O TCGA-E2-A1L8 TCGA-E2-A572 TCGA-LL-A442 
        9.70        10.42        50.79        73.64        39.72        29.23 
TCGA-LL-A50Y TCGA-S3-AA12 TCGA-3C-AAAU TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SG 
       25.05        18.87       133.05        48.46         9.96        14.27 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0ER TCGA-A2-A0ET 
       18.21       143.15       121.94        77.19        74.40        35.05 
TCGA-A2-A0SU TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25C 
       54.64        32.55        50.47        17.36        60.72        17.19 
TCGA-A2-A25E TCGA-A2-A4S0 TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IY 
      105.34        23.21        30.61        25.15        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Y 
       10.59        10.29        13.41        13.02        13.02        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-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       18.05        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T 
       40.01         9.99        12.00        33.07        25.02        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3TN 
       27.02        38.04        22.95        99.35        26.04        14.99 
TCGA-AC-A3YJ TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A7VB TCGA-AC-A8OR 
       24.79        14.96        11.44        17.42         8.22         1.32 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FF 
        0.33         0.33         0.23         2.96         6.44         5.65 
TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A03P 
        7.00         0.33         0.33         0.30         0.33        95.70 
TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B 
       21.40        20.32        22.36       113.62       108.72        98.27 
TCGA-AO-A12C TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H 
       77.98        40.57        97.08        61.87        11.51        24.79 
TCGA-AQ-A1H2 TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 
       15.62         5.26        75.22        55.86       107.24        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24R 
      134.14        37.81        61.28        50.89        94.22       112.77 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A2LK TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      105.30        98.66        54.21       275.87       129.57        50.70 
TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP 
      127.33       165.76       234.28        81.17        78.02       102.77 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC 
      188.68        79.46       206.86        28.27        68.94        43.59 
TCGA-BH-A0AU TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0E1 TCGA-BH-A0E7 
       62.93        49.94        90.97        81.73        15.68        44.81 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       24.49        63.32        15.16        24.56        41.00        52.96 
TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HW TCGA-BH-A0W3 
       20.38         2.37        16.96         2.50        51.32        23.93 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1FD TCGA-BH-A1FG 
       26.66        37.74        66.05       113.82        33.17       122.83 
TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A42T TCGA-BH-A6R8 TCGA-C8-A12M 
       63.35        53.98        83.31        10.52         9.63        11.77 
TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
       11.77        12.66        48.53        12.33        11.34        11.28 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       12.95        12.33        20.25        15.45        16.87        24.56 
TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS 
       12.95        13.25        18.15        18.90        18.97        12.20 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC 
       13.32        18.58        17.79        16.73        27.58        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       17.16        15.22        14.73        55.30        15.85        16.31 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y1 TCGA-D8-A27E TCGA-D8-A27W TCGA-D8-A73W 
       12.99        15.16         9.93        17.42        12.26        12.66 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A14O 
       43.00        83.54        46.59        40.41        37.51        44.68 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       33.17        75.98        32.02        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       23.87        21.63        18.21        12.92        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1IG 
       20.58        56.94        14.07        51.39        33.01        70.36 
TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A56Z 
       59.18        22.19        60.36        19.66        24.59         8.28 
TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1NG TCGA-E9-A1NH 
       30.61        34.29        34.82        36.82        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
        9.86         2.56         3.02        11.15        48.23        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 
        1.12        46.65        21.27        47.64        34.45        42.25 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS 
       37.74        38.37        40.50        38.99        24.56        29.72 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP 
       38.07        32.91        23.90        23.84        25.81        26.40 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 
       18.90        28.77        29.95        41.13        23.11        18.48 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A6SA TCGA-GM-A2DC 
       18.90        10.52        52.73        22.09        16.77        83.34 
TCGA-GM-A2DM TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A66H 
      106.06        15.32         2.63        12.36        31.99        26.70 
TCGA-OL-A66O TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-AA11 TCGA-V7-A7HQ TCGA-Z7-A8R6 
       17.36        47.01         0.16        13.84        66.84       107.05 

$subtype2
TCGA-A2-A04Y TCGA-A7-A26H TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08S TCGA-A8-A09I 
       36.13        23.80        15.06        33.01        33.01        45.07 
TCGA-AQ-A0Y5 TCGA-B6-A0I8 TCGA-E2-A2P5 TCGA-3C-AALI TCGA-A1-A0SI TCGA-A1-A0SK 
        5.65        24.62        26.99       131.67        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CW TCGA-A2-A0CX 
        7.96        39.32       101.98        55.43       107.93        56.81 
TCGA-A2-A0CY TCGA-A2-A0D1 TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG 
       55.00        34.55        31.82        27.12        44.88        21.90 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A25B TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A4SF 
       21.67        23.77        42.44        26.96        21.90        17.92 
TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 
       14.73        10.42         1.02        17.98        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A08B 
       53.98        43.00        18.97        14.01         9.99        38.01 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A097 
       37.05         9.99        31.00       112.08        30.97        12.00 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09W TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH 
        1.02         8.98         0.99        19.23         5.72        33.04 
TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AC-A7VC TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        6.48        16.80         0.03         9.96         7.36         0.16 
TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XW 
        0.33         7.04         0.33         0.33        12.33         5.59 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AR-A0TW TCGA-AR-A1AT 
       66.77        81.63        71.80       130.09        98.93        41.82 
TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A254 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RH 
      160.90        89.00        85.64        11.90       146.50       212.25 
TCGA-B6-A0RO TCGA-B6-A0WW TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B4 
      162.05        18.35       139.17        68.12       103.63        39.16 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0H7 
       76.60        77.75        74.14        46.39        16.27        23.08 
TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18U 
       12.89        50.79        20.12        90.84        30.28        51.39 
TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 
       69.93        12.00        49.58        17.69        31.53        25.08 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W 
       45.63        72.07        26.14        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM 
       12.56        12.16        12.46        12.49        10.92        12.33 
TCGA-C8-A274 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       16.70        12.49        56.81        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XJ 
       15.78        20.09        20.38        21.01        23.90        21.83 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27N TCGA-D8-A27R TCGA-E2-A107 
       16.54        15.32        14.14        17.06        10.09        34.42 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A9RU 
       40.11        28.44        34.26        69.96        23.34        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 
       17.52        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-A2-A25A TCGA-A7-A426 TCGA-A7-A5ZX TCGA-AR-A1AM TCGA-BH-A0DO TCGA-LD-A74U 
      107.70        11.97        11.05        98.33        54.05        13.22 
TCGA-LL-A440 TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-A1-A0SE TCGA-A1-A0SH 
       24.95        11.41       108.07        47.61        43.43        47.24 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES 
      114.81        92.48       107.93        53.13        80.28        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G6 TCGA-A2-A3KD 
       61.94        24.72        19.33        48.46        16.47        39.65 
TCGA-A2-A4RY TCGA-A7-A0CG TCGA-A7-A13H TCGA-A7-A5ZW TCGA-A8-A0A4 TCGA-AC-A23G 
       21.30        34.29        29.56        10.72        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        20.45        97.68 
TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
      118.59       105.27        50.96        63.62        38.17        40.54 
TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-BH-A0AZ 
       38.96       112.37       129.07       140.28       169.51        63.09 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0DP TCGA-BH-A0E9 
       37.22        21.70        61.68        72.23        15.65        81.83 
TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A18M TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O 
       13.61        24.95        72.56        33.99        28.14        36.82 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A3M7 TCGA-D8-A3Z5 
      110.60        20.88        18.87        21.76        33.99        33.37 
TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A1IF TCGA-E2-A1IJ 
       21.67        38.24        43.33        20.71        37.41        28.44 
TCGA-E2-A1L6 TCGA-EW-A1J2 TCGA-EW-A1PG TCGA-GM-A3XG TCGA-GM-A5PV TCGA-HN-A2OB 
       54.18        13.25        34.55        43.73        13.55        62.47 
TCGA-LD-A7W6 TCGA-MS-A51U TCGA-OL-A5RV TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY 
       13.28        22.39        34.92        19.73        40.11         0.26 
TCGA-S3-AA14 
       17.39 

$subtype4
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A8-A07E TCGA-AC-A3W6 
       48.56        48.36        31.36        11.28        19.99        19.79 
TCGA-AC-A5XS TCGA-AQ-A7U7 TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0EA TCGA-BH-A18H 
       19.33        19.20        73.35        81.63        32.58        21.44 
TCGA-D8-A146 TCGA-E2-A1BC TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-GM-A2DO TCGA-OL-A5RU 
       21.14        16.47        15.68        52.96        85.35        40.08 
TCGA-S3-AA17 TCGA-WT-AB41 TCGA-4H-AAAK TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SJ 
       13.94        52.96        11.44        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       134.40       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-A425 TCGA-A7-A4SA TCGA-A7-A4SB 
       35.47        37.45        33.11        14.70        14.93        13.74 
TCGA-A7-A4SC TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A095 
       14.66        18.97        12.00        12.00        31.00        41.98 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A6 
        9.99        50.04        15.02        12.00        19.04        21.04 
TCGA-A8-A0AB TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FO TCGA-AC-A2QI 
       17.03        22.26        40.57        86.66        74.14        19.33 
TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A4ZE TCGA-AC-A6IV 
       32.45        14.83        24.13        25.05        29.26        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A0FN 
       12.26         1.68        20.19         0.33         0.62         7.17 
TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV 
        6.90         0.36         5.36         0.33         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J5 
       80.28        61.35        68.75        69.83        44.42        26.04 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       53.03        21.53        50.86        72.00        65.10        26.24 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12G TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TT 
      102.31        70.42        53.88        32.52        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-A5QN TCGA-B6-A0I5 
       71.05       166.42        86.53        39.39        33.30       281.29 
TCGA-B6-A0IE TCGA-B6-A0IN TCGA-B6-A0RG TCGA-B6-A0RN TCGA-B6-A0WS TCGA-B6-A0WY 
       65.52        84.59        68.45       263.28        97.48       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C 
      129.70        58.55        73.51       170.17        85.35        71.15 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B5 TCGA-BH-A0B8 TCGA-BH-A0BC 
       25.55        81.44        37.74        70.22        51.58        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 
       18.21        43.53        75.48        74.14        85.87        41.75 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       89.06        77.98        67.10        38.01        29.98        13.91 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E2 
        3.22         2.56        79.00        67.86        70.88        14.30 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HB TCGA-BH-A0HF 
       30.35        10.78        63.39        53.26        26.50        23.90 
TCGA-BH-A0HK TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
        5.85        36.85        27.25        42.35        44.81        32.91 
TCGA-BH-A18I TCGA-BH-A18R TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       35.93        37.55        91.99        82.85        42.28        55.69 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FL TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 
      120.62        74.73        55.00       130.16        36.79        20.12 
TCGA-BH-A5J0 TCGA-BH-AB28 TCGA-C8-A132 TCGA-C8-A26W TCGA-C8-A8HR TCGA-D8-A141 
       23.51         9.44        12.59        12.53        13.41        20.58 
TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1XB 
       13.48        55.50        14.01        14.70        25.74        18.15 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27I 
       19.92        17.69        15.52        14.24        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z6 
       48.03        16.41         1.61        13.08        12.53        18.51 
TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Z TCGA-E2-A15C 
       16.18        25.22        27.52        28.87        18.51        22.82 
TCGA-E2-A15D TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B5 
       17.29        55.63        11.05        19.56        87.22        32.35 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       37.25        77.65        33.73         3.88        60.99        11.08 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 
       34.55        43.56        32.88        35.77        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A249 TCGA-E9-A295 
       34.95        45.01        32.05        41.03         7.13        12.33 
TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        9.47        30.44        26.70        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P1 
        8.48        18.21        16.57        25.94        40.41        39.78 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6SC 
       13.94        14.43        25.91        34.03        23.51        31.30 
TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN 
      216.76        72.10        85.15        86.96       115.69       101.62 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-LD-A66U 
      110.50        38.20        66.38        72.03        18.12        21.24 
TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A7SZ TCGA-OK-A5Q2 TCGA-OL-A5DA 
        7.10        17.06        14.70        19.53         2.10        58.62 
TCGA-OL-A5RX TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DD 
       28.87        65.62        41.92        42.77        26.04        64.21 
TCGA-PE-A5DE TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-XX-A899 TCGA-XX-A89A 
       86.96        18.48        21.07        15.35        16.04 

$subtype5
TCGA-A1-A0SP TCGA-A7-A26F TCGA-A7-A26I TCGA-AC-A62X TCGA-AQ-A54N TCGA-AR-A1AR 
       19.20        24.26        21.73        13.71         2.56        17.23 
TCGA-AR-A2LR TCGA-E2-A158 TCGA-E2-A1LG TCGA-LL-A5YP TCGA-A1-A0SB TCGA-A1-A0SO 
       57.27        14.79        50.07        14.79         8.52        28.01 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 
       18.02        78.41        73.84        87.25        24.79        67.33 
TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE 
       33.76        99.19        50.43        17.52         8.38        18.21 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT 
       18.61        31.73        19.20        10.59        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE 
       29.98        47.31        35.93        50.83        24.39        35.31 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        31.73        20.19        23.74        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O 
       12.10        10.29         9.37         8.75        33.99         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AC-A6IW 
        8.98        24.99         0.99        73.05        14.66        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        60.56 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 
       82.62        26.93       140.55        84.10        23.31        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AY 
      107.21       125.16       108.36       101.00        99.32        33.73 
TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
      104.28        99.62        93.83        10.59        77.62       143.38 
TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU 
       32.58       233.62       140.88       255.68        89.46       282.90 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 
       21.01       245.10       101.52        37.87         7.07        74.99 
TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
       18.84        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-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 
        4.90        55.63         7.36        51.16        25.81        97.48 
TCGA-BH-A1FC TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ 
      114.15        18.64         5.26        12.66        12.59         0.16 
TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK 
       14.43        13.97        19.20        20.09        19.40        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N 
       16.41        43.04        16.04        13.05        13.48        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A1AZ 
       38.60        31.96        69.34        63.62        25.05        76.57 
TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.50        33.70       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       52.73        34.92        38.76        34.16        39.55        41.62 
TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW 
       40.73        20.12         0.69        30.18         0.79        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A3U0 
       29.82        30.08         7.86        19.99        19.96        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-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-AC-A3W5 TCGA-GM-A2DD TCGA-LL-A740 TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A3XV 
       16.57        75.02        14.50        63.29        17.13        32.75 
TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04C TCGA-AO-A0J2 TCGA-AO-A0JE 
       43.00        14.01         0.99         1.78        32.78        76.77 
TCGA-AO-A12D TCGA-AR-A0TX TCGA-AR-A1AO TCGA-AR-A24U TCGA-AR-A2LH TCGA-B6-A0IK 
       82.68        64.83        86.07       102.84        20.25        18.77 
TCGA-B6-A0RS TCGA-BH-A0AW TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A1FU TCGA-BH-A203 
      100.70        20.45        84.13        31.00        55.50        38.60 
TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A135 
       57.83        11.93        11.77        12.66        13.51        12.92 
TCGA-C8-A1HK TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A8HP 
       12.03        12.36        12.95         0.03         9.76        13.02 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT 
       20.88        14.17        12.03        53.00        20.12        16.64 
TCGA-E2-A14P TCGA-E2-A1B0 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E9-A1RH TCGA-E9-A248 
       40.96        53.62        75.81        28.90        46.59         1.94 
TCGA-EW-A6SD TCGA-GM-A2DB TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YO TCGA-LL-A73Z 
       33.21        79.10        11.84        10.62        14.47         7.46 
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   169.51   281.29   282.90   102.84 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  25.480   23.080   38.170   32.520   28.355   20.185 
[1] "0.2 - 275.9 (25.5)" "0.0 - 212.2 (23.1)" "0.3 - 169.5 (38.2)"
[4] "0.3 - 281.3 (32.5)" "0.2 - 282.9 (28.4)" "0.0 - 102.8 (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        94        75         1
  subtype2       7        8        0        1        51        38         0
  subtype3       7        9        1        1        17        27         0
  subtype4      42       25        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 X
  subtype1         43         13          7        4       6
  subtype2         31          8         12        7       2
  subtype3         14          1         12        1       0
  subtype4         44          0         23        3       5
  subtype5         17          4          5        3       1
  subtype6          7          1          6        2       0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          20        7        7       42       13        1
  STAGE IA         23        8        9       25       15        5
  STAGE IB          4        0        1        1        0        0
  STAGE II          2        1        1        1        1        0
  STAGE IIA        94       51       17       87       86       23
  STAGE IIB        75       38       27       62       41       13
  STAGE III         1        0        0        0        0        1
  STAGE IIIA       43       31       14       44       17        7
  STAGE IIIB       13        8        1        0        4        1
  STAGE IIIC        7       12       12       23        5        6
  STAGE IV          4        7        1        3        3        2
  STAGE X           6        2        0        5        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  76 170  28  18
  subtype2  25 110  21  10
  subtype3  25  38  27   1
  subtype4  95 156  41   2
  subtype5  40 124  17   6
  subtype6  18  35   4   3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       76       25       25       95       40       18
  T2      170      110       38      156      124       35
  T3       28       21       27       41       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  70   1
  subtype4 235   3
  subtype5 162   4
  subtype6  52   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  250    5
  subtype2  134    7
  subtype3   70    1
  subtype4  235    3
  subtype5  162    4
  subtype6   52    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      250      134       70      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 129 143
  subtype2  70  74
  subtype3  42  44
  subtype4 106 168
  subtype5  72  99
  subtype6  26  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  129  143
  subtype2   70   74
  subtype3   42   44
  subtype4  106  168
  subtype5   72   99
  subtype6   26   25
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO       129       70       42      106       72       26
  YES      143       74       44      168       99       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                            27
  subtype4                          0                           176
  subtype5                          1                           163
  subtype6                          0                            54
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             24                   0
  subtype2                             16                   0
  subtype3                             56                   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                                8
  subtype5                     5                                2
  subtype6                     1                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                 15             21
  subtype2                  1              4
  subtype3                  1              2
  subtype4                  0              9
  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       27      176      163
  INFILTRATING LOBULAR CARCINOMA         24       16       56      100        2
  MEDULLARY CARCINOMA                     0        0        0        1        5
  METAPLASTIC CARCINOMA                   0        3        0        0        5
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        4        5        8        2
  MUCINOUS CARCINOMA                     15        1        1        0        0
  OTHER, SPECIFY                         21        4        2        9        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 118  20
  subtype2 229  40
  subtype3 184  22
  subtype4 190  28
  subtype5 155  30
  subtype6  40   7
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     138      269      206      218      185       47 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      20       40       22       28       30        7 
$subtype1
TCGA-A7-A2KD TCGA-A8-A06U TCGA-A8-A09K TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-E2-A15O 
       22.32        29.03        29.98        66.15        81.63        50.79 
TCGA-GM-A2DD TCGA-GM-A2DO TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A2-A0CW TCGA-A2-A0SV 
       75.02        85.35       133.05        13.68       107.93        27.12 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3XZ 
       23.47        17.36        42.44        18.15       105.34        50.37 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A8-A08J 
       30.61        37.45        25.15        10.29        13.41        37.05 
TCGA-AC-A23H TCGA-AC-A2QI TCGA-AC-A3YJ TCGA-AC-A7VB TCGA-AO-A03M TCGA-AO-A03O 
        5.72        19.33        24.79         8.22        61.35        81.63 
TCGA-AO-A0J3 TCGA-AO-A0JB TCGA-AO-A0JM TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A24H 
       21.40        50.70        71.80        11.51        98.33       160.90 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LK 
      112.77        97.84        98.66        85.64       166.42        54.21 
TCGA-B6-A0IA TCGA-B6-A0IN TCGA-B6-A0RL TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
      275.87        84.59        81.17        62.93        20.45        25.55 
TCGA-BH-A0B1 TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0HA TCGA-BH-A0HB 
       37.74        41.75        90.97        67.10        52.96        26.50 
TCGA-BH-A18L TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FN TCGA-BH-A204 
       26.66       113.82        12.00        55.69        72.07        83.31 
TCGA-BH-A209 TCGA-BH-A6R8 TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A138 
      130.16         9.63        12.66        48.53        12.16        12.49 
TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.34        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 
       12.53        15.45        16.87         0.03        24.56        12.95 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1Y3 TCGA-D8-A27N 
       56.81        13.25        17.79        27.58        14.14        17.06 
TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O 
       10.09        12.26        18.51        43.00        46.59        44.68 
TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A155 TCGA-E2-A15K TCGA-E2-A15S TCGA-E2-A1B5 
       75.98        18.51        21.04         9.04        14.07        32.35 
TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A2P6 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N9 
       60.36        28.90        34.55        34.82        36.82        36.20 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
       34.95         6.12        11.15        40.24        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22H 
       21.27        42.25        39.09        38.37        41.03        40.50 
TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX 
        0.69        29.72        32.91        28.77        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A2FS TCGA-EW-A2FV 
       29.85        41.13        23.11        18.90        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DA 
       22.09        15.22        16.77        31.30        59.57       216.76 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-S3-A6ZF 
       83.34        72.10        15.32        19.53        12.36        18.81 

$subtype2
TCGA-A1-A0SP TCGA-A2-A04V TCGA-A7-A26F TCGA-A8-A08S TCGA-A8-A09I TCGA-AC-A5EI 
       19.20        63.12        24.26        33.01        45.07        14.53 
TCGA-AC-A62X TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A1AR TCGA-AR-A2LR TCGA-E2-A158 
       13.71         5.65         2.56        17.23        57.27        14.79 
TCGA-E2-A1LG TCGA-LL-A5YP TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SO 
       50.07        14.79       131.67        48.46        31.79        28.01 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CL 
       18.02        78.41        73.84        87.25        55.43        99.12 
TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ 
       24.79        55.00        67.33        34.55        33.76        79.76 
TCGA-A2-A0EV TCGA-A2-A0ST TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 
       31.82        99.19        44.88        50.43        17.52         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F 
       20.75        21.90        21.67        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-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D 
        7.30        24.39        26.96        21.90        35.31        31.73 
TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       20.19        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       10.29         9.37         8.75        13.02         1.02        17.98 
TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O 
        9.01        33.99        18.97        14.01        32.05         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08L TCGA-A8-A08R 
        8.98        24.99         9.99        18.05         9.99         0.99 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09Q TCGA-A8-A0A7 TCGA-AC-A2BK TCGA-AC-A2QH 
       12.00         9.99        25.02         0.99        73.05        33.04 
TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04A 
       16.80        11.44        13.58         1.12         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         7.36         7.46         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        0.33         7.96         7.59         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.53         0.33        12.33 
TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL 
        0.33        68.75        32.78        52.18        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
      115.27       108.03        82.68        60.56        61.87        82.62 
TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A0U3 
       26.93       140.55        84.10       109.02        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24K 
      107.21       125.16       108.36        99.32        33.73        50.89 
TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
      104.28        99.62        93.83        10.59        77.62       143.38 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS 
       32.58        11.90       233.62       140.88       255.68       100.70 
TCGA-B6-A0RT TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A3ZX 
       89.46        21.01       113.79        58.55       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 
        7.07        74.99        18.84        59.84        39.55        51.68 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0DD TCGA-BH-A0DL 
       43.53        61.51        77.75        77.95        81.73        78.28 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA 
        4.41         9.63        31.00        30.35         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
        4.90        55.63        37.55         7.36        51.39        51.16 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P 
       97.48       114.15        38.60        18.64        11.93        11.77 
TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A278 
       12.66        13.51        12.59        10.92         0.16         9.76 
TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA 
       14.43        20.88        13.97        14.17        19.20        16.50 
TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X5 
       15.78        53.00        20.09        20.12        20.09        18.58 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1XW 
       21.83        14.50        19.92        16.41        15.16        43.04 
TCGA-D8-A1XZ TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14P TCGA-E2-A14R 
       15.32        16.04        13.05        13.48        40.96        38.60 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 
       34.26        32.02        31.96        69.34        63.62        25.05 
TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LH 
       23.34        76.57        53.62        28.50        33.70       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 
      102.61         8.75        34.92        38.76        17.69        34.16 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A243 
       36.56        41.62        32.09        46.59        40.73        20.12 
TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
        1.94        30.18         0.79        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-A3XL TCGA-HN-A2NL TCGA-LL-A5YO 
       33.21       109.87        79.10        69.30         2.60        14.47 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5RW 
       16.08        15.68        19.59        36.30        58.52        36.36 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A97C 
       22.32        20.38        23.47        14.07        28.21         8.91 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-UU-A93S 
        9.93        20.68        19.27        17.03         3.81 

$subtype3
TCGA-5L-AAT0 TCGA-A2-A0CQ TCGA-A7-A0CD TCGA-A7-A26H TCGA-A7-A426 TCGA-A7-A5ZX 
       48.56        88.60        38.30        23.80        11.97        11.05 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09C TCGA-AC-A5XS TCGA-AO-A0JI TCGA-AQ-A54O 
       33.01        17.95         1.02        19.33        50.24        32.91 
TCGA-AR-A5QM TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A572 
       73.35        21.44        89.16         9.70        10.42        39.72 
TCGA-EW-A1P3 TCGA-LL-A442 TCGA-LL-A50Y TCGA-S3-AA12 TCGA-S3-AA17 TCGA-3C-AALK 
       52.96        29.23        25.05        18.87        13.94        47.61 
TCGA-5T-A9QA TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CT 
        9.96         7.96        18.21       143.15       121.94        75.25 
TCGA-A2-A0CU TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU 
        5.19        25.22       101.72        74.40        35.05        34.29 
TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       24.72        44.28        20.52        32.55        25.28        50.47 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A4S0 TCGA-A2-A4S2 
       48.46        23.77        60.72        52.47        23.21        21.14 
TCGA-A7-A0DC TCGA-A7-A3IZ TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A6VX 
       29.79        10.59        14.70        14.93        13.74        10.42 
TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S 
       13.02        26.01         1.02        12.00        10.98         7.99 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A09D TCGA-A8-A09M 
       36.95        13.02         0.99        19.96        50.04        33.07 
TCGA-A8-A09R TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM 
        8.98        19.04        13.02        27.02        17.03        99.35 
TCGA-AC-A3TN TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A8OR TCGA-AN-A041 
       14.99        29.26        14.96        17.42         1.32         0.23 
TCGA-AN-A046 TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         5.65         7.00         7.17         6.90 
TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L 
        5.36         0.30         0.33         0.33         5.33        80.28 
TCGA-AO-A03T TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A0JJ 
       69.83        20.32        53.03        21.53        26.24        62.04 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12G TCGA-AO-A12H TCGA-AQ-A04H 
      113.62       106.78        98.27        53.88        40.57        24.79 
TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A24L TCGA-B6-A0IC TCGA-B6-A0RG TCGA-B6-A0RM 
       75.22       107.24        94.22        50.70        68.45        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ 
      263.28       162.05       188.68        79.46        18.35       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 
      129.70        28.27        68.94        43.59        73.51        68.12 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0DH TCGA-BH-A0DK 
       37.22        32.02        18.21        21.70        38.01        13.91 
TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GZ TCGA-BH-A0HL 
        3.22        15.68        14.30        44.81        10.78         2.37 
TCGA-BH-A0HO TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I 
        2.50        51.32        27.25        23.93        44.81        35.93 
TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1FG TCGA-BH-A1FR TCGA-BH-A42T TCGA-BH-A5J0 
       37.74        66.05       122.83        53.98        10.52        23.51 
TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A274 TCGA-C8-A9FZ TCGA-D8-A145 TCGA-D8-A1X8 
       11.77        12.66        16.70        19.46        13.48        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1Y2 
       23.90        12.39        17.16        14.73        17.69        14.24 
TCGA-D8-A27E TCGA-D8-A3Z5 TCGA-D8-A73W TCGA-E2-A106 TCGA-E2-A10A TCGA-E2-A14S 
       17.42        33.37        12.66        83.54        40.41        33.17 
TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15R 
       23.87        21.63        55.63        53.92        20.58        56.94 
TCGA-E2-A15T TCGA-E2-A56Z TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1R3 TCGA-E9-A1RD 
       51.39         8.28        34.29        32.88         2.56         1.12 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A24A TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       47.64        34.45        24.56        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1J1 TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       25.81        27.85        18.90        34.03        17.52        23.51 
TCGA-GI-A2C8 TCGA-GM-A2DM TCGA-GM-A3NW TCGA-LD-A66U TCGA-LL-A6FP TCGA-LL-A9Q3 
        7.40       106.06       110.50        21.24        22.26        17.49 
TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A66H TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       27.91        58.62        26.70        42.77        26.04        17.36 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG 
       40.11        47.01        64.21        86.96         0.16        18.48 
TCGA-S3-AA11 TCGA-V7-A7HQ 
       13.84        66.84 

$subtype4
TCGA-5L-AAT1 TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A3J1 TCGA-AC-A3W6 TCGA-AQ-A7U7 
       48.36       107.70        31.36        11.28        19.79        19.20 
TCGA-AR-A1AM TCGA-BH-A0DO TCGA-BH-A0EA TCGA-D8-A146 TCGA-E2-A1BC TCGA-E2-A2P5 
       98.33        54.05        32.58        21.14        16.47        26.99 
TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A740 TCGA-OL-A5RU TCGA-WT-AB41 TCGA-Z7-A8R5 
       13.22        24.95        14.50        40.08        52.96       108.07 
TCGA-4H-AAAK TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR 
       11.44        14.37        48.10       136.73       114.81       107.93 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW 
       98.99        53.13       134.40       118.45        72.00        61.94 
TCGA-A2-A0T1 TCGA-A2-A0T6 TCGA-A2-A0YK TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A3KC 
       17.13        18.90        19.33        20.25        16.47        36.23 
TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A4RY TCGA-A7-A0CG TCGA-A7-A0DB 
       39.65        56.28        35.93        21.30        34.29        33.11 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A8-A095 
       29.56        23.74        11.34        14.66        10.72        41.98 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.91        22.26        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       87.12        26.04        74.14        14.66        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A3YI 
       14.83        22.19        24.13        25.05        15.48        23.24 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AO-A0JF 
       18.67        12.26         0.03        20.19         2.30        65.10 
TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AR-A0TY TCGA-AR-A1AJ TCGA-AR-A1AK 
       70.42        20.45        32.52        55.86       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24P 
       97.68        86.07        94.29        86.43       118.59         2.76 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
      105.27        50.96        93.30        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        65.52 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A2IU TCGA-B6-A401 
      112.37        18.77       140.28       282.90       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BL TCGA-BH-A0BO 
      103.63        71.15        63.09        70.22        74.89        72.23 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DV 
       74.14        89.06        77.98        29.98        79.00        67.86 
TCGA-BH-A0E9 TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F 
       81.83        63.39        13.61        24.95        42.35        32.91 
TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FB 
       72.56        91.99        42.28        49.58        25.81       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q 
       74.73        33.99        55.50        28.14        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.12       110.60        20.88         5.26        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12V TCGA-C8-A132 TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A3M7 
        9.44        12.66        12.59        12.36        12.95        33.99 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU 
       13.02        12.49        13.41        55.50        14.01        14.70 
TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T 
       13.45        14.43        48.03        16.41         1.61        13.08 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q 
       21.67        16.18        27.52        28.87        47.15        38.24 
TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1IH 
       43.33        20.71        11.05        19.56        87.22        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1L6 TCGA-E2-A1LL TCGA-E2-A3DX TCGA-E9-A1NE 
       28.44        59.18        54.18        43.04        43.56        35.77 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A227 TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 
       24.82        28.27        32.05        12.33         9.47        30.44 
TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PF TCGA-EW-A1PG 
       12.20        13.25        39.78        30.08        14.43        34.55 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A3XG 
       70.85        85.15        86.96       115.69       101.62        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
       11.57         7.10        13.28        10.62        32.75        17.06 
TCGA-LL-A73Z TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
        7.46        22.39         2.10        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-XX-A899 TCGA-XX-A89A 
       15.35        16.04 

$subtype5
TCGA-A2-A04Y TCGA-A2-A1G4 TCGA-A7-A13G TCGA-A7-A26I TCGA-A8-A06T TCGA-A8-A09E 
       36.13        19.56        23.61        21.73        53.06        49.05 
TCGA-AO-A1KT TCGA-B6-A0I8 TCGA-E2-A1L8 TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SH 
       17.79        24.62        73.64         8.52        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0SU 
       20.88        39.32       101.98        77.19        61.58        54.64 
TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YI TCGA-A2-A1FZ TCGA-A2-A25C TCGA-A7-A0CH 
       49.84        17.46        49.48        22.45        17.19        35.47 
TCGA-A7-A0DA TCGA-A8-A07B TCGA-A8-A07Z TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08T 
       35.67        43.00        45.07        12.00        31.00       112.08 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09N TCGA-A8-A09T 
       43.00        30.97         9.99        12.00         1.02        19.04 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       14.01        12.00        21.04        38.04        19.23        22.95 
TCGA-AN-A03X TCGA-AN-A049 TCGA-AN-A0AS TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03U 
        0.33         0.62         0.33         0.33         5.59        58.95 
TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A126 
       44.42        26.04        50.86        72.00        76.77       108.72 
TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A1KP TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TR 
      102.31        77.98        97.08       130.09        15.62         5.26 
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-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A250 
       86.53       120.33       102.84       105.30        98.76        89.00 
TCGA-AR-A255 TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RP 
       71.05       127.33       165.76       129.07       234.28       102.77 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B8 
      169.51        97.48        81.44        39.16        84.13        51.58 
TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        75.48        74.14        76.60        85.87        49.94 
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        63.32        15.16 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HF TCGA-BH-A0HI 
       53.26        24.56        23.08        41.00        23.90        20.38 
TCGA-BH-A0HK TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A1EN 
        5.85        12.89        50.79        20.12        30.28        69.93 
TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FJ TCGA-BH-A1FL 
       82.85        17.69        31.53        25.08        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A208 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
       45.63        26.14        57.83        11.77        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-D8-A141 TCGA-D8-A1J8 
       12.56        12.92        12.33        11.28        20.58        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JN 
       17.49        18.15        18.90        12.03        18.97        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF 
       21.01        12.20        13.32        16.73        18.15        15.22 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY 
       55.30        15.85        16.31        16.64        12.99        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 
       15.52         9.93        12.53        37.51        28.44        23.24 
TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1B4 TCGA-E2-A1IE TCGA-E2-A1IF 
       19.43        17.29        18.21        33.01        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L9 
       70.36         3.88        22.19        60.99        11.08        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LS TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NG 
       24.59        75.81        52.73        22.29        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A229 
       18.94         9.86         3.02        48.23        45.01        37.74 
TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       41.72        38.99         7.13        39.72         8.48        18.21 
TCGA-EW-A1J3 TCGA-EW-A1OZ TCGA-EW-A1P6 TCGA-EW-A1PD TCGA-EW-A1PE 
       16.57        40.41        18.48        13.94        10.52 

$subtype6
TCGA-A8-A07E TCGA-A8-A084 TCGA-AC-A3W5 TCGA-EW-A1J5 TCGA-W8-A86G TCGA-A1-A0SE 
       19.99        15.06        16.57        15.68        11.41        43.43 
TCGA-A2-A0CP TCGA-A2-A0EO TCGA-A2-A0EY TCGA-A7-A26J TCGA-A8-A075 TCGA-A8-A076 
       92.48        80.28        63.29        20.61        17.03        53.98 
TCGA-A8-A07F TCGA-A8-A08B TCGA-A8-A08Z TCGA-AC-A3EH TCGA-AC-A6NO TCGA-AN-A0AJ 
       18.97        38.01        40.01         6.48         1.68         9.96 
TCGA-AO-A03N TCGA-AO-A0J8 TCGA-AR-A24N TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0IG 
       66.77        22.36        99.78       281.29       129.57       146.50 
TCGA-B6-A0RH TCGA-B6-A1KN TCGA-BH-A0C1 TCGA-BH-A0HN TCGA-BH-A0HQ TCGA-BH-A18K 
      212.25       139.17        46.39        16.96        36.85        90.84 
TCGA-C8-A137 TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A152 TCGA-E2-A15C 
       12.46        25.22        34.42        40.11        69.96        22.82 
TCGA-E2-A15H TCGA-E2-A1BD TCGA-E2-A570 TCGA-E9-A5UP TCGA-GM-A3NY TCGA-LL-A5YN 
       12.92        37.25        30.61        26.40        38.20        14.70 
TCGA-LL-A6FQ TCGA-OL-A5D8 TCGA-OL-A66K TCGA-WT-AB44 TCGA-Z7-A8R6 
        2.63        31.99        41.92        29.03       107.05 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.16     0.16     0.03     0.33     1.68 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  275.87   255.68   263.28   282.90   234.28   281.29 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  29.900   24.260   25.135   32.830   26.140   34.420 
[1] "0.0 - 275.9 (29.9)" "0.2 - 255.7 (24.3)" "0.2 - 263.3 (25.1)"
[4] "0.0 - 282.9 (32.8)" "0.3 - 234.3 (26.1)" "1.7 - 281.3 (34.4)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      14        6        0        1        44        35         1
  subtype2      10       17        1        1       117        57         0
  subtype3      13       22        3        1        66        47         0
  subtype4      23       19        1        2        53        59         1
  subtype5      23       17        1        1        59        38         0
  subtype6       6        4        1        0        14        14         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         24          2          9        2       2
  subtype2         37          7         12        8       3
  subtype3         31          8         15        1       4
  subtype4         33          3         20        3       0
  subtype5         25          5          7        5       4
  subtype6          3          1          1        1       1
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          14       10       13       23       23        6
  STAGE IA          6       17       22       19       17        4
  STAGE IB          0        1        3        1        1        1
  STAGE II          1        1        1        2        1        0
  STAGE IIA        44      117       66       53       59       14
  STAGE IIB        35       57       47       59       38       14
  STAGE III         1        0        0        1        0        0
  STAGE IIIA       24       37       31       33       25        3
  STAGE IIIB        2        7        8        3        5        1
  STAGE IIIC        9       12       15       20        7        1
  STAGE IV          2        8        1        3        5        1
  STAGE X           2        3        4        0        4        1
[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  31  85  19   4
  subtype2  45 191  26  11
  subtype3  55 118  28   9
  subtype4  70 102  43   3
  subtype5  66  99  12  10
  subtype6  12  25   7   3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       31       45       55       70       66       12
  T2       85      191      118      102       99       25
  T3       19       26       28       43       12        7
  T4        4       11        9        3       10        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  58  49  18  10
  subtype2 146  74  34  15
  subtype3  99  68  24  15
  subtype4  93  85  18  21
  subtype5  86  66  21  10
  subtype6  26  14   3   4
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       58      146       99       93       86       26
  N1       49       74       68       85       66       14
  N2       18       34       24       18       21        3
  N3       10       15       15       21       10        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"
D9V6, binary
          cls
clus         0   1
  subtype1 120   2
  subtype2 230   8
  subtype3 170   2
  subtype4 165   3
  subtype5 164   5
  subtype6  38   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  120    2
  subtype2  230    8
  subtype3  170    2
  subtype4  165    3
  subtype5  164    5
  subtype6   38    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      120      230      170      165      164       38
  1        2        8        2        3        5        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"
D9V7, binary
          cls
clus         0   1
  subtype1 139   1
  subtype2 270   4
  subtype3 208   3
  subtype4 218   0
  subtype5 183   4
  subtype6  47   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139    1
  subtype2  270    4
  subtype3  208    3
  subtype4  218    0
  subtype5  183    4
  subtype6   47    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      139      270      208      218      183       47
  MALE          1        4        3        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"
D9V8, binary
          cls
clus         0   1
  subtype1  61  70
  subtype2 111 135
  subtype3  84 111
  subtype4  86 117
  subtype5  79  87
  subtype6  20  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   70
  subtype2  111  135
  subtype3   84  111
  subtype4   86  117
  subtype5   79   87
  subtype6   20   23
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        61      111       84       86       79       20
  YES       70      135      111      117       87       23
[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                           106
  subtype2                          1                           245
  subtype3                          0                           135
  subtype4                          0                            95
  subtype5                          0                           154
  subtype6                          0                            33
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             17                   1
  subtype2                              4                   5
  subtype3                             48                   0
  subtype4                            106                   0
  subtype5                             14                   0
  subtype6                             11                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                5
  subtype2                     5                                3
  subtype3                     0                                7
  subtype4                     4                                5
  subtype5                     0                                8
  subtype6                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  4              7
  subtype2                  1              9
  subtype3                  9             12
  subtype4                  3              5
  subtype5                  0             11
  subtype6                  0              2
D9V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         106      245      135       95      154
  INFILTRATING LOBULAR CARCINOMA         17        4       48      106       14
  MEDULLARY CARCINOMA                     1        5        0        0        0
  METAPLASTIC CARCINOMA                   0        5        0        4        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        5        3        7        5        8
  MUCINOUS CARCINOMA                      4        1        9        3        0
  OTHER, SPECIFY                          7        9       12        5       11
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          33
  INFILTRATING LOBULAR CARCINOMA         11
  MEDULLARY CARCINOMA                     0
  METAPLASTIC CARCINOMA                   0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      0
  OTHER, SPECIFY                          2
[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"
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    17                        21
  subtype2                                0    11                        81
  subtype3                                0     8                        37
  subtype4                                1    13                        29
  subtype5                                0    11                         7
  subtype6                                0     1                         7
          vv
clus       WHITE
  subtype1    97
  subtype2   156
  subtype3   141
  subtype4   171
  subtype5   148
  subtype6    32
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                  17       11        8       13       11
  BLACK OR AFRICAN AMERICAN              21       81       37       29        7
  WHITE                                  97      156      141      171      148
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   1
  BLACK OR AFRICAN AMERICAN               7
  WHITE                                  32
[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"
D9V12, binary
          cls
clus         0   1
  subtype1   9 122
  subtype2   6 222
  subtype3   8 161
  subtype4   9 193
  subtype5   7 137
  subtype6   0  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  122
  subtype2    6  222
  subtype3    8  161
  subtype4    9  193
  subtype5    7  137
  subtype6    0   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            9        6        8        9        7        0
  NOT HISPANIC OR LATINO      122      222      161      193      137       38
[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(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  53  12
  subtype2  97  23
  subtype3 167  20
  subtype4 162  22
  subtype5  66   6
  subtype6  97  20
  subtype7 134  27
  subtype8  69   4
  subtype9  71  13
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      65      120      187      184       72      117      161       73 
subtype9 
      84 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12       23       20       22        6       20       27        4 
subtype9 
      13 
$subtype1
TCGA-AO-A0JI TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       50.24       133.05        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A4S0 TCGA-A7-A0D9 TCGA-A7-A3J0 TCGA-A7-A3RF 
       60.72        42.44        23.21        37.45        10.29        13.41 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AN-A04A TCGA-AO-A0J3 TCGA-AR-A0U2 TCGA-AR-A252 
       14.96        11.44         2.96        21.40        83.87        93.30 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A1KC TCGA-BH-A0B8 
       84.59       165.76       113.79        28.27        43.59        51.58 
TCGA-BH-A0HL TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 
        2.37        27.25        26.66        45.63        53.98        83.31 
TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HO TCGA-C8-A27A 
       11.77        12.66        11.34        11.28        12.33        24.56 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XU 
       56.81        13.25        12.39        15.22        14.73        12.99 
TCGA-D8-A1XV TCGA-D8-A1Y3 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14T TCGA-E2-A155 
       15.16        14.14        43.00        46.59        75.98        21.04 
TCGA-E2-A15A TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IG 
       23.34        56.94        14.07        51.39        77.65        70.36 
TCGA-E2-A1L7 TCGA-E9-A1N3 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R5 TCGA-E9-A1RE 
       60.36        34.82        36.56        35.24         3.02        46.65 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A3Q9 TCGA-EW-A6SA 
       42.25        38.37        38.99        32.91        16.77 

$subtype2
TCGA-A2-A04Y TCGA-A7-A26I TCGA-A8-A084 TCGA-A8-A08S TCGA-A8-A09I TCGA-AC-A5EI 
       36.13        21.73        15.06        33.01        45.07        14.53 
TCGA-B6-A0I8 TCGA-E2-A2P5 TCGA-GM-A2DD TCGA-3C-AALI TCGA-A1-A0SM TCGA-A2-A04W 
       24.62        26.99        75.02       131.67         7.96       101.98 
TCGA-A2-A04X TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T1 
       55.43       107.93        34.55        79.76        44.88        17.13 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A8-A06Q TCGA-A8-A076 
       21.90        21.67        32.75        56.28         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08X 
        9.01        43.00        14.01        37.05         9.99        43.00 
TCGA-A8-A09D TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH 
       50.04        14.01         0.99        19.23         5.72        33.04 
TCGA-AC-A2QJ TCGA-AC-A7VC TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A0AK TCGA-AN-A0AM 
       14.66         0.03         0.33         0.33         7.36         0.16 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0JE 
        7.04         0.33        61.35        44.42        32.78        76.77 
TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24U 
       82.68       130.09        64.83        37.81        50.89       102.84 
TCGA-AR-A24Z TCGA-AR-A255 TCGA-B6-A0IG TCGA-BH-A0AW TCGA-BH-A0BF TCGA-BH-A0BP 
       98.66        71.05       146.50        20.45        43.53        75.48 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DX TCGA-BH-A0DZ 
       89.06        81.73        13.91        78.28        70.88        16.27 
TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A18K TCGA-BH-A18R TCGA-BH-A1EV 
       31.00        23.08        41.00        90.84        37.55        12.00 
TCGA-BH-A1F2 TCGA-BH-A202 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12Y 
       31.53        26.14       130.16        11.93        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A26X 
       12.56        13.51        12.92        10.92        12.03        12.36 
TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF 
        0.03        20.88        14.17        17.49        16.50        12.03 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1XT TCGA-E2-A10C TCGA-E2-A14Z 
       53.00        20.09        20.38        16.64        40.11        18.51 
TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A1B0 
       69.96        25.05        20.71         9.04        11.05        53.62 
TCGA-E2-A1IN TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E9-A1N6 TCGA-E9-A1NG TCGA-E9-A1R4 
       22.19        75.81        28.90        22.29        25.84         6.12 
TCGA-E9-A1RA TCGA-E9-A226 TCGA-E9-A22E TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SD 
       45.01        34.45        41.72        25.91        17.52        33.21 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YO TCGA-OL-A5RZ TCGA-OL-A97C 
       79.10        72.10        11.84        14.47        22.32         8.91 

$subtype3
TCGA-A2-A25A TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A5ZX 
      107.70        31.36        22.32        11.28        11.97        11.05 
TCGA-A8-A07E TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A5QM 
       19.99        16.57        19.79        19.20        98.33        73.35 
TCGA-BH-A0DO TCGA-E2-A572 TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A740 TCGA-OL-A5RU 
       54.05        39.72        13.22        24.95        14.50        40.08 
TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALK TCGA-4H-AAAK TCGA-A2-A0CO TCGA-A2-A0CP 
       11.41       108.07        47.61        11.44       114.81        92.48 
TCGA-A2-A0CR TCGA-A2-A0CZ TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0YD 
      107.93        53.13       118.45        72.00        61.94        25.28 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G6 TCGA-A2-A3KC TCGA-A2-A3KD 
       49.48        19.33        48.46        16.47        36.23        39.65 
TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A425 
       21.30        21.14        34.29        33.11        29.56        14.70 
TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB 
       14.66        10.72        21.04        73.91        22.26        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QI TCGA-AC-A3BB 
       86.66        90.71        60.92        87.12        19.33        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A6IV TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AO-A0JA 
       15.48        23.24        18.67        20.19         2.30        21.53 
TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A128 TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AR-A1AL 
       65.10        62.04       106.78        20.45        32.52        97.68 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A2LH 
      118.59         2.76       105.27        50.96        85.64        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QP 
       86.53        63.62        38.17        39.39        40.54        38.96 
TCGA-B6-A0IH TCGA-B6-A0RQ TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0BA TCGA-BH-A0BM 
      112.37       140.28        85.35        71.15        37.22        61.68 
TCGA-BH-A0BO TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI 
       72.23        49.94        74.14        46.39        67.10        29.98 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E9 TCGA-BH-A0H3 TCGA-BH-A0HI TCGA-BH-A0HP 
       79.00        67.86        81.83        63.39        20.38        13.61 
TCGA-BH-A0W4 TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1FB 
       24.95        35.93        72.56        42.28        49.58       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       74.73        33.99        28.14        36.82        36.79        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      110.60        20.88         5.26        18.87        21.76         9.44 
TCGA-C8-A12P TCGA-C8-A274 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A1JB 
       11.77        16.70        33.99        12.95        13.41        55.50 
TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P 
       14.01        14.70        14.43        48.03        16.41         1.61 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.53        33.37        18.51        21.67        16.18 
TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15C TCGA-E2-A1B1 
       25.22        34.42        38.24        43.33        22.82        87.22 
TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1QZ 
       37.41        33.73        28.44        54.18        43.56        24.82 
TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1J2 TCGA-EW-A1PG TCGA-EW-A3E8 
        9.47        30.44        26.70        13.25        34.55        34.03 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A3NY 
       23.51        59.57        85.15       115.69       101.62        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-MS-A51U TCGA-OL-A5D6 
       11.57        21.24        13.28        10.62        22.39        36.30 
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-A6VQ TCGA-PE-A5DC TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA14 TCGA-XX-A899 
       19.73        47.01         0.26        18.48        17.39        15.35 
TCGA-XX-A89A 
       16.04 

$subtype4
TCGA-5L-AAT0 TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A8-A06T TCGA-A8-A091 TCGA-AQ-A54O 
       48.56        19.56        38.30        53.06        33.01        32.91 
TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-D8-A146 TCGA-E2-A1BC TCGA-LL-A442 
       89.16         9.70        10.42        21.14        16.47        29.23 
TCGA-S3-AA12 TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SQ 
       18.87        14.37        14.27        20.88        13.68        18.21 
TCGA-A2-A04R TCGA-A2-A0CK TCGA-A2-A0CU TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER 
      121.94       136.73         5.19        25.22       101.72        74.40 
TCGA-A2-A0ET TCGA-A2-A0SU TCGA-A2-A0T4 TCGA-A2-A0YF TCGA-A2-A1FZ TCGA-A2-A1G0 
       35.05        54.64        20.52        50.47        22.45        20.25 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A7-A0CH TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A3IY 
       17.19       105.34        35.47        29.79        25.15        11.34 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A8-A06P TCGA-A8-A06Z TCGA-A8-A07J 
       14.93        13.74        14.73        13.02         1.02        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 
       32.05        10.98         7.99        45.07        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A1 
        0.99        19.96        12.00        25.02         8.98        12.00 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AC-A4ZE TCGA-AC-A62Y TCGA-AC-A8OR 
       27.02        38.04        99.35        29.26        17.42         1.32 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XP 
        0.23         0.62         7.00         7.17         6.90         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03R TCGA-AO-A03T 
        0.33         0.33         5.33        80.28        68.75        69.83 
TCGA-AO-A0J7 TCGA-AO-A0JG TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12E 
       20.32        26.24        71.80       108.72        98.27        70.42 
TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A1AK 
       40.57        61.87        24.79        98.33        75.22       103.86 
TCGA-AR-A1AN TCGA-AR-A24M TCGA-AR-A24R TCGA-AR-A24V TCGA-B6-A0IA TCGA-B6-A0IC 
       96.00       120.33       112.77       105.30       275.87        50.70 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
       18.77       127.33       129.07        68.45       234.28        78.02 
TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0X0 TCGA-B6-A0X5 
      102.77       169.51        97.48       188.68       129.70        68.94 
TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0C0 TCGA-BH-A0DE 
       73.51        63.09        18.21        21.70        41.75        77.98 
TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0H0 
       38.01         3.22        15.68        44.81        63.32        15.16 
TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HW 
       24.56        52.96        23.90         5.85         2.50        51.32 
TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1ET 
       50.79        23.93        37.74        66.05       113.82        82.85 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A42T TCGA-BH-A6R8 TCGA-C8-A12X TCGA-D8-A145 
      122.83        63.35        10.52         9.63        12.66        13.48 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XD 
       18.90        18.97        13.32        17.79        16.73        17.16 
TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XY TCGA-D8-A27E TCGA-D8-A73W 
       19.92        55.30        15.85        16.54        17.42        12.66 
TCGA-E2-A106 TCGA-E2-A10A TCGA-E2-A14S TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15I 
       83.54        40.41        33.17        23.87        21.63        55.63 
TCGA-E2-A15P TCGA-E2-A1B4 TCGA-E2-A1IK TCGA-E9-A1NE TCGA-E9-A1R2 TCGA-E9-A1R7 
       19.56        33.01        59.18        35.77        34.95        48.23 
TCGA-E9-A1RB TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22H 
       32.09        47.64        32.05        37.74        41.03        40.50 
TCGA-E9-A24A TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1J1 
       24.56        23.90        23.84        25.81        39.72        18.90 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       29.95        41.13        23.11        13.94        10.52        14.43 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2DM TCGA-OL-A5DA 
       52.73        22.09        31.30         7.40       106.06        58.62 
TCGA-OL-A6VR TCGA-PE-A5DE TCGA-PL-A8LX TCGA-V7-A7HQ 
       40.11        86.96         0.16        66.84 

$subtype5
TCGA-5L-AAT1 TCGA-A8-A09C TCGA-EW-A1J5 TCGA-EW-A1P3 TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         1.02        15.68        52.96        43.43        48.10 
TCGA-A1-A0SH TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EN 
       47.24        39.32        77.19        98.99        61.58       134.40 
TCGA-A2-A0EY TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A7-A26J TCGA-A8-A08Z 
       63.29        17.46        18.90        20.75        20.61        40.01 
TCGA-A8-A09N TCGA-AC-A23E TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AC-A6NO TCGA-AN-A03Y 
        1.02        22.95         6.48        16.80         1.68         0.33 
TCGA-AN-A0FD TCGA-AO-A03N TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A12A TCGA-AR-A0U3 
        6.44        66.77        53.03        72.00       102.31       134.14 
TCGA-AR-A1AP TCGA-AR-A24N TCGA-B6-A0I5 TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A1KN 
       93.90        99.78       281.29       212.25       162.05       139.17 
TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BQ TCGA-BH-A0BR 
       68.12       103.63        81.44        70.22        74.14        76.60 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0HQ TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18J 
       15.65         2.56        36.85        42.35        44.81        20.12 
TCGA-BH-A18P TCGA-BH-A1EY TCGA-C8-A138 TCGA-C8-A278 TCGA-D8-A1XB TCGA-D8-A1XS 
       30.28        17.69        12.49         9.76        18.15        16.31 
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-A1BD TCGA-E2-A1IU TCGA-E2-A570 TCGA-E9-A1NH TCGA-E9-A1RC TCGA-E9-A249 
       37.25        11.08        30.61        18.94        40.24         7.13 
TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-LL-A5YN TCGA-S3-A6ZF TCGA-Z7-A8R6 
       12.20         8.48        16.57        14.70        18.81       107.05 

$subtype6
TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A7-A13G TCGA-A8-A093 TCGA-A8-A09E TCGA-AO-A1KT 
       63.12        88.60        23.61        17.95        49.05        17.79 
TCGA-BH-A0B6 TCGA-BH-A0EA TCGA-BH-A18H TCGA-E2-A15O TCGA-E2-A1L8 TCGA-S3-AA17 
       81.63        32.58        21.44        50.79        73.64        13.94 
TCGA-5T-A9QA TCGA-A2-A0CT TCGA-A2-A0EO TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T3 
        9.96        75.25        80.28        24.72        44.28        49.84 
TCGA-A7-A0CJ TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A08O 
       30.61        13.02        26.01        18.97        18.97        31.00 
TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
      112.08        30.97        41.98         9.99         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0AB TCGA-AC-A3YJ 
       33.07        19.04        19.04        13.02        17.03        24.79 
TCGA-AN-A0AS TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03O 
        0.33         5.36        12.33         0.33         5.59        81.63 
TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A125 TCGA-AO-A12C 
       26.04        22.36        50.70        50.86       113.62        77.98 
TCGA-AO-A12G TCGA-AO-A1KP TCGA-AQ-A1H2 TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A1AT 
       53.88        97.08        15.62         5.26       107.24        41.82 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24X TCGA-AR-A250 
       61.28        86.53       160.90        94.22        98.76        89.00 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0WV TCGA-B6-A0WW 
      129.57        65.52        81.17       263.28        79.46        18.35 
TCGA-B6-A0WZ TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0BC 
      206.86        62.93        25.55        37.74        39.16        32.02 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0C7 TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0HB 
       85.87        77.75        90.97        10.78        53.26        26.50 
TCGA-BH-A0HN TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EW 
       16.96        12.89        32.91        69.93        91.99        55.69 
TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A132 TCGA-C8-A1HE 
       25.08        55.00        11.77        12.66        12.59        12.33 
TCGA-C8-A1HM TCGA-D8-A141 TCGA-D8-A1JD TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 
       12.33        20.58        18.15        21.01        12.20        18.58 
TCGA-D8-A1XA TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A15G 
       27.58        15.52         9.93        28.44        44.68        18.21 
TCGA-E2-A15J TCGA-E2-A1B5 TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E9-A1N5 
       53.92        32.35         3.88        60.99        19.66        36.82 
TCGA-E9-A1N9 TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RG TCGA-EW-A1IZ TCGA-EW-A1J6 
       36.20         9.86        11.15        21.27        18.21        28.77 
TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P6 
       25.94        40.41        18.48 

$subtype7
TCGA-A1-A0SP TCGA-A7-A26F TCGA-AC-A62X TCGA-AQ-A54N TCGA-AR-A1AR TCGA-AR-A2LR 
       19.20        24.26        13.71         2.56        17.23        57.27 
TCGA-E2-A158 TCGA-E2-A1LG TCGA-LL-A5YP TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO 
       14.79        50.07        14.79         8.52        31.79        28.01 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 
       18.02        78.41        73.84        87.25        24.79        67.33 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YM TCGA-A2-A25F 
       99.19        50.43        17.52         8.38        31.73        10.59 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       33.93        91.07        29.98        47.31        35.93        50.37 
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-A26G TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       23.74        21.17        12.10        10.29         9.37         8.75 
TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK 
       33.99         9.99         8.98        24.99         0.99        73.05 
TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0FJ TCGA-AN-A0FL 
       13.58         1.12         1.71         7.46         7.96         7.59 
TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 
        0.33         0.53         0.33        58.95        52.18        37.48 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AR-A0TP 
       55.33       108.03        60.56        82.62        26.93       140.55 
TCGA-AR-A0TS TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO 
       84.10       107.21       125.16       108.36       101.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-B6-A0I1 
       99.32        33.73       104.28        99.62        93.83        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS 
      143.38        32.58       233.62       140.88       255.68       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A3ZX 
       89.46       282.90        21.01        58.55       101.52        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0BL 
        7.07        74.99        18.84        59.84        51.68        74.89 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q 
        4.41         9.63         5.59        23.05         4.90        55.63 
TCGA-BH-A18T TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A5IZ 
        7.36        25.81        97.48       114.15        55.50        18.64 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A147 
       12.66        12.66        12.59         0.16        14.43        19.20 
TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H 
       20.09        14.50        16.41        43.04        16.04        13.05 
TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A1AZ 
       13.48        47.15        38.60        31.96        69.34        76.57 
TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A573 
       28.50        33.70       102.61         8.75        52.73        34.92 
TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA 
       34.16        41.62        40.73        20.12         0.69        30.18 
TCGA-EW-A1OW TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB 
       22.82        39.78        29.82        30.08         7.86        19.99 
TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL 
       17.49        24.99       109.87        70.85        69.30         2.60 
TCGA-LL-A441 TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
       32.75        16.08        58.52        36.36        20.38        23.47 
TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       28.21         9.93        20.68        19.27        17.26 

$subtype8
TCGA-A7-A26H TCGA-AR-A2LL TCGA-GM-A2DO TCGA-LL-A50Y TCGA-WT-AB41 TCGA-A2-A04N 
       23.80        66.15        85.35        25.05        52.96       143.15 
TCGA-A2-A0EU TCGA-A2-A0YC TCGA-A2-A259 TCGA-A2-A25D TCGA-A7-A3IZ TCGA-A7-A4SF 
       34.29        32.55        52.47        18.15        10.59        17.92 
TCGA-A7-A6VX TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A7VB TCGA-AN-A0FF TCGA-AR-A2LE 
       10.42        26.04        74.14         8.22         5.65       166.42 
TCGA-AR-A2LK TCGA-AR-A5QN TCGA-B6-A2IU TCGA-BH-A0E2 TCGA-BH-A5J0 TCGA-C8-A137 
       54.21        33.30       170.17        14.30        23.51        12.46 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A8HQ TCGA-C8-A9FZ 
       20.25        12.53        15.45        16.87        12.49        19.46 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27G 
       25.74        23.90        21.83        17.69        14.24        13.45 
TCGA-D8-A27N TCGA-D8-A27W TCGA-E2-A108 TCGA-E2-A15L TCGA-E2-A2P6 TCGA-E2-A56Z 
       17.06        12.26        27.52        20.58        34.55         8.28 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RD 
       34.29        17.69        32.88        28.27         2.56         1.12 
TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1PA 
       39.09        12.33        29.72        26.40        27.85        18.90 
TCGA-EW-A6S9 TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A3NW TCGA-LD-A7W5 TCGA-LL-A5YM 
       15.22        83.34        86.96       110.50         7.10        15.32 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       22.26         2.63        19.53        12.36        17.49        27.91 
TCGA-OL-A5D8 TCGA-OL-A66H TCGA-OL-A66O TCGA-PE-A5DD TCGA-S3-A6ZH TCGA-S3-AA11 
       31.99        26.70        17.36        64.21        21.07        13.84 
TCGA-UU-A93S 
        3.81 

$subtype9
TCGA-A8-A06U TCGA-A8-A09K TCGA-AC-A5XS TCGA-AQ-A0Y5 TCGA-A2-A0CL TCGA-A2-A0CY 
       29.03        29.98        19.33         5.65        99.12        55.00 
TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A1G1 TCGA-A2-A4RW TCGA-A2-A4S1 
       33.76        31.82        27.12        19.20         7.30        26.96 
TCGA-A2-A4S3 TCGA-A7-A4SD TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A07W TCGA-A8-A082 
       21.90        14.50        17.98        17.03         9.99        18.05 
TCGA-A8-A08B TCGA-A8-A097 TCGA-AC-A6IX TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AR 
       38.01        12.00        12.26         1.78         9.96         0.33 
TCGA-AN-A0AT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AO-A124 
        0.33         0.36         0.33         0.33         0.33       115.27 
TCGA-AO-A1KS TCGA-AR-A0TT TCGA-AR-A0TY TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24S 
       11.51       109.02        55.86        94.29        86.43        97.84 
TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BW 
       10.59        11.90        39.55        84.13        61.51        77.95 
TCGA-BH-A0GY TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A208 
       30.35        51.39        51.16        72.07        38.60        57.83 
TCGA-C8-A130 TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A8HP TCGA-D8-A142 TCGA-D8-A143 
       12.16        12.95        12.95        13.02        13.97        14.17 
TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1XZ TCGA-D8-A27R TCGA-E2-A14P TCGA-E2-A14W 
       15.78        20.12        15.32        10.09        40.96        32.02 
TCGA-E2-A150 TCGA-E2-A15H TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A574 
       63.62        12.92        24.59       106.75        43.04        38.76 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1OY TCGA-EW-A1PC 
        6.58        46.59         1.94         0.79        29.85         6.15 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-GM-A2DA TCGA-LL-A5YL TCGA-LL-A73Y TCGA-LL-A73Z 
       19.96        55.00       216.76        17.06        15.68         7.46 
TCGA-LL-A8F5 TCGA-OK-A5Q2 TCGA-OL-A66N TCGA-OL-A66P TCGA-UL-AAZ6 TCGA-WT-AB44 
       19.59         2.10        26.04        14.07        17.03        29.03 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    2.37     0.03     0.26     0.16     0.33     0.33     0.16     1.12 
subtype9 
    0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  165.76   146.50   140.28   275.87   281.29   263.28   282.90   170.17 
subtype9 
  216.76 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  32.910   25.875   33.370   29.525   35.555   28.770   30.180   21.070 
subtype9 
  19.460 
[1] "2.4 - 165.8 (32.9)" "0.0 - 146.5 (25.9)" "0.3 - 140.3 (33.4)"
[4] "0.2 - 275.9 (29.5)" "0.3 - 281.3 (35.6)" "0.3 - 263.3 (28.8)"
[7] "0.2 - 282.9 (30.2)" "1.1 - 170.2 (21.1)" "0.3 - 216.8 (19.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        5        0        1        17        20         0
  subtype2      13        6        1        1        43        30         0
  subtype3      17       18        1        1        38        50         1
  subtype4      17       18        2        0        60        46         0
  subtype5      12        3        1        0        22        17         0
  subtype6       8       10        1        1        48        17         0
  subtype7      11       15        0        1        74        31         0
  subtype8       4        6        1        0        22        19         1
  subtype9       5        4        0        1        29        20         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         13          4          3        1       2
  subtype2         13          3          9        2       1
  subtype3         35          1         22        1       1
  subtype4         32          7          1        1       3
  subtype5          5          2          6        3       1
  subtype6         17          3          3        4       4
  subtype7         14          4          6        3       2
  subtype8          9          2          8        1       0
  subtype9         15          0          6        4       0
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           2       13       17       17       12        8       11
  STAGE IA          5        6       18       18        3       10       15
  STAGE IB          0        1        1        2        1        1        0
  STAGE II          1        1        1        0        0        1        1
  STAGE IIA        17       43       38       60       22       48       74
  STAGE IIB        20       30       50       46       17       17       31
  STAGE III         0        0        1        0        0        0        0
  STAGE IIIA       13       13       35       32        5       17       14
  STAGE IIIB        4        3        1        7        2        3        4
  STAGE IIIC        3        9       22        1        6        3        6
  STAGE IV          1        2        1        1        3        4        3
  STAGE X           2        1        1        3        1        4        2
            clus
vv           subtype8 subtype9
  STAGE I           4        5
  STAGE IA          6        4
  STAGE IB          1        0
  STAGE II          0        1
  STAGE IIA        22       29
  STAGE IIB        19       20
  STAGE III         1        0
  STAGE IIIA        9       15
  STAGE IIIB        2        0
  STAGE IIIC        8        6
  STAGE IV          1        4
  STAGE X           0        0
[1] 12  9
[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  11  42  10   4
  subtype2  33  74  11   6
  subtype3  53  85  47   2
  subtype4  59  97  23   8
  subtype5  18  44   5   6
  subtype6  33  71   8   5
  subtype7  39 105  12   6
  subtype8  17  44   9   3
  subtype9  16  58  10   0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1       11       33       53       59       18       33       39       17
  T2       42       74       85       97       44       71      105       44
  T3       10       11       47       23        5        8       12        9
  T4        4        6        2        8        6        5        6        3
    clus
vv   subtype9
  T1       16
  T2       58
  T3       10
  T4        0
[1] 4 9
[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  26  26  11   3
  subtype2  57  39  14  11
  subtype3  78  65  20  24
  subtype4  87  74  21   1
  subtype5  40  20   5   8
  subtype6  54  41  12   6
  subtype7 100  43  12   7
  subtype8  29  25   8   9
  subtype9  37  23  15   6
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0       26       57       78       87       40       54      100       29
  N1       26       39       65       74       20       41       43       25
  N2       11       14       20       21        5       12       12        8
  N3        3       11       24        1        8        6        7        9
    clus
vv   subtype9
  N0       37
  N1       23
  N2       15
  N3        6
[1] 4 9
[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  62   1
  subtype2 112   2
  subtype3 135   1
  subtype4 160   1
  subtype5  62   3
  subtype6  99   5
  subtype7 139   3
  subtype8  54   1
  subtype9  64   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62    1
  subtype2  112    2
  subtype3  135    1
  subtype4  160    1
  subtype5   62    3
  subtype6   99    5
  subtype7  139    3
  subtype8   54    1
  subtype9   64    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       62      112      135      160       62       99      139       54
  1        1        2        1        1        3        5        3        1
   clus
vv  subtype9
  0       64
  1        4
[1] 2 9
[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  66   2
  subtype2 122   2
  subtype3 187   0
  subtype4 184   4
  subtype5  72   1
  subtype6 115   2
  subtype7 163   0
  subtype8  73   0
  subtype9  83   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66    2
  subtype2  122    2
  subtype3  187    0
  subtype4  184    4
  subtype5   72    1
  subtype6  115    2
  subtype7  163    0
  subtype8   73    0
  subtype9   83    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       66      122      187      184       72      115      163
  MALE          2        2        0        4        1        2        0
        clus
vv       subtype8 subtype9
  FEMALE       73       83
  MALE          0        1
[1] 2 9
[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  34  27
  subtype2  47  63
  subtype3  74 105
  subtype4  78  90
  subtype5  31  31
  subtype6  47  64
  subtype7  64  81
  subtype8  32  41
  subtype9  34  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   27
  subtype2   47   63
  subtype3   74  105
  subtype4   78   90
  subtype5   31   31
  subtype6   47   64
  subtype7   64   81
  subtype8   32   41
  subtype9   34   41
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        34       47       74       78       31       47       64       32
  YES       27       63      105       90       31       64       81       41
     clus
vv    subtype9
  NO        34
  YES       41
[1] 2 9
[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                            51
  subtype2                          0                           107
  subtype3                          0                            68
  subtype4                          0                           138
  subtype5                          0                            56
  subtype6                          0                            92
  subtype7                          1                           143
  subtype8                          0                            42
  subtype9                          0                            71
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              4                   0
  subtype2                              7                   1
  subtype3                            110                   0
  subtype4                             20                   0
  subtype5                             13                   0
  subtype6                             12                   0
  subtype7                              2                   5
  subtype8                             24                   0
  subtype9                              8                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                4
  subtype2                     3                                1
  subtype3                     1                                4
  subtype4                     0                                6
  subtype5                     0                                3
  subtype6                     0                                7
  subtype7                     2                                2
  subtype8                     0                                2
  subtype9                     3                                0
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  5              4
  subtype2                  0              5
  subtype3                  1              3
  subtype4                  8             16
  subtype5                  0              1
  subtype6                  0              6
  subtype7                  0              7
  subtype8                  3              2
  subtype9                  0              2
D10V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA          51      107       68      138       56
  INFILTRATING LOBULAR CARCINOMA          4        7      110       20       13
  MEDULLARY CARCINOMA                     0        1        0        0        0
  METAPLASTIC CARCINOMA                   0        3        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        4        1        4        6        3
  MUCINOUS CARCINOMA                      5        0        1        8        0
  OTHER, SPECIFY                          4        5        3       16        1
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  INFILTRATING CARCINOMA NOS              0        1        0        0
  INFILTRATING DUCTAL CARCINOMA          92      143       42       71
  INFILTRATING LOBULAR CARCINOMA         12        2       24        8
  MEDULLARY CARCINOMA                     0        5        0        0
  METAPLASTIC CARCINOMA                   0        2        0        3
  MIXED HISTOLOGY (PLEASE SPECIFY)        7        2        2        0
  MUCINOUS CARCINOMA                      0        0        3        0
  OTHER, SPECIFY                          6        7        2        2
[1] 8 9
[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                                0     6                         5
  subtype2                                1    13                        12
  subtype3                                0     8                        25
  subtype4                                0     7                        22
  subtype5                                0     4                         8
  subtype6                                0     5                        12
  subtype7                                0     7                        60
  subtype8                                0     7                        24
  subtype9                                0     4                        14
          vv
clus       WHITE
  subtype1    56
  subtype2    80
  subtype3   151
  subtype4   133
  subtype5    57
  subtype6    82
  subtype7    89
  subtype8    41
  subtype9    56
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                   6       13        8        7        4
  BLACK OR AFRICAN AMERICAN               5       12       25       22        8
  WHITE                                  56       80      151      133       57
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0
  ASIAN                                   5        7        7        4
  BLACK OR AFRICAN AMERICAN              12       60       24       14
  WHITE                                  82       89       41       56
[1] 4 9
[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   0  64
  subtype2   4  87
  subtype3   4 165
  subtype4  12 136
  subtype5   4  59
  subtype6   4  86
  subtype7   5 138
  subtype8   4  68
  subtype9   2  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   64
  subtype2    4   87
  subtype3    4  165
  subtype4   12  136
  subtype5    4   59
  subtype6    4   86
  subtype7    5  138
  subtype8    4   68
  subtype9    2   70
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        4        4       12        4        4
  NOT HISPANIC OR LATINO       64       87      165      136       59       86
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            5        4        2
  NOT HISPANIC OR LATINO      138       68       70
[1] 2 9
[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 117  17
  subtype2  86   8
  subtype3  50   9
  subtype4 102  19
  subtype5 125  17
  subtype6  98  16
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     134       94       59      121      142      114 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      17        8        9       19       17       16 
$subtype1
TCGA-A7-A13G TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A15O TCGA-EW-A1J5 
       23.61        89.16         9.70        10.42        50.79        15.68 
TCGA-LL-A442 TCGA-S3-AA12 TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A2-A0CW 
       29.23        18.87       133.05       131.67         9.96       107.93 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XV TCGA-A2-A4S0 TCGA-A7-A13F 
       23.47        17.36        42.44        32.75        23.21        25.15 
TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SF TCGA-A7-A6VX 
       20.61        10.59        10.29        13.41        17.92        10.42 
TCGA-AC-A23H TCGA-AC-A3EH TCGA-AC-A3YJ TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
        5.72         6.48        24.79         1.68         8.22         1.32 
TCGA-AO-A12H TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A24H 
       40.57        11.51        15.62        93.90        61.28       160.90 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LK 
      120.33        99.78       112.77        98.66        89.00        54.21 
TCGA-BH-A0BS TCGA-BH-A0DG TCGA-BH-A0HA TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A18K 
       85.87        67.10        52.96         2.37        16.96        90.84 
TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EY 
       26.66        66.05        69.93       113.82        12.00        17.69 
TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A204 TCGA-BH-A6R8 TCGA-C8-A12N TCGA-C8-A12U 
       25.08        45.63        83.31         9.63        11.77        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HK TCGA-C8-A1HN 
       12.66        48.53        12.46        12.49        12.03        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M8 
       12.33        20.25        15.45        16.70        24.56        12.95 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JI 
       19.46        56.81        13.25        14.17        17.49        18.97 
TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XF 
       12.20        18.58        17.79        27.58        12.39        15.22 
TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10A 
       15.85        15.16        17.42        12.53        18.51        40.41 
TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15C TCGA-E2-A15E 
       44.68        75.98        32.02        69.96        22.82        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1LB TCGA-E9-A1N3 
       18.21        12.92        56.94        51.39        75.81        34.82 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       34.95         6.12        11.15        40.24         1.12        46.65 
TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A3Q9 TCGA-E9-A5UO 
       34.45        42.25        41.03        40.50        32.91        25.81 
TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ 
       26.40        18.90        16.57        28.77        25.94        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P6 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-GM-A3NY TCGA-LL-A7T0 
       41.13        18.48        15.22        16.77        38.20        12.36 
TCGA-LL-A9Q3 TCGA-OL-A5D8 TCGA-OL-A5RZ TCGA-S3-A6ZF TCGA-S3-AA11 TCGA-UL-AAZ6 
       17.49        31.99        22.32        18.81        13.84        17.03 
TCGA-V7-A7HQ TCGA-Z7-A8R6 
       66.84       107.05 

$subtype2
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A7-A5ZX TCGA-AC-A5XS TCGA-AQ-A54O TCGA-AR-A5QM 
       48.56        48.36        11.05        19.33        32.91        73.35 
TCGA-BH-A0DO TCGA-E2-A572 TCGA-LL-A440 TCGA-LL-A50Y TCGA-OL-A5RU TCGA-S3-AA17 
       54.05        39.72        24.95        25.05        40.08        13.94 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R5 TCGA-3C-AALJ TCGA-3C-AALK TCGA-A2-A4RW 
       11.41        52.96       108.07        48.46        47.61         7.30 
TCGA-A2-A4RY TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A425 TCGA-A7-A4SA 
       21.30        26.96        21.14        21.90        14.70        14.93 
TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A56D TCGA-A7-A5ZW TCGA-AC-A4ZE TCGA-AC-A5XU 
       13.74        14.66        14.73        10.72        29.26        14.96 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AR-A5QN TCGA-AR-A5QP 
       11.44        17.42        20.19         2.30        33.30        38.96 
TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
       68.12        18.84        10.52       110.60        20.88        23.51 
TCGA-BH-A8FZ TCGA-BH-AB28 TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14S 
       18.87         9.44        33.37        21.67        38.24        33.17 
TCGA-E2-A15F TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A54Y TCGA-E9-A5FK 
       21.63         8.28        30.61        34.29        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6SC TCGA-GM-A3XG 
        0.79        27.85        34.03        23.51        31.30        43.73 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A7W6 
       72.03        13.55        18.12        62.47        21.24        13.28 
TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
       32.75        17.06        15.32        14.70        22.26         2.63 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5DA TCGA-OL-A5RV 
       27.91        22.39         2.10        36.30        58.62        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       28.87        24.72        26.70        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       26.04        19.73        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-UU-A93S TCGA-WT-AB44 TCGA-XX-A899 
        0.26         3.81        29.03        15.35 

$subtype3
TCGA-A7-A26E TCGA-AC-A5EI TCGA-E2-A1BC TCGA-LL-A740 TCGA-4H-AAAK TCGA-A1-A0SB 
       31.36        14.53        16.47        14.50        11.44         8.52 
TCGA-A1-A0SI TCGA-A2-A04W TCGA-A7-A0DB TCGA-AC-A23G TCGA-AC-A2QH TCGA-AC-A2QJ 
       20.88       101.98        33.11        73.91        33.04        14.66 
TCGA-AC-A3TN TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A24V 
       14.99        15.48        16.80        96.00        86.07       105.30 
TCGA-B6-A0IH TCGA-B6-A0RH TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AZ 
      112.37       212.25       103.63        71.15        62.93        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DX TCGA-BH-A0EI 
       81.44        70.22        90.97        29.98        70.88        63.32 
TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1FB TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A208 
       72.56        91.99       120.62        33.99        28.14        57.83 
TCGA-BH-A6R9 TCGA-C8-A12O TCGA-D8-A13Z TCGA-D8-A1JD TCGA-D8-A1JU TCGA-D8-A1XB 
        5.26        12.66        20.88        18.15        14.70        18.15 
TCGA-D8-A1XU TCGA-D8-A73X TCGA-E2-A153 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BD 
       12.99        25.22        23.24        87.22        33.01        37.25 
TCGA-E2-A1IJ TCGA-E2-A1IN TCGA-E9-A22E TCGA-EW-A1IW TCGA-EW-A2FR TCGA-GM-A3XN 
       28.44        22.19        41.72        12.20        55.00        66.38 
TCGA-JL-A3YW TCGA-LD-A9QF TCGA-OL-A97C TCGA-S3-AA14 TCGA-XX-A89A 
       11.84        10.62         8.91        17.39        16.04 

$subtype4
TCGA-A2-A1G4 TCGA-AO-A1KT TCGA-BH-A18H TCGA-D8-A146 TCGA-E2-A1L8 TCGA-A1-A0SD 
       19.56        17.79        21.44        21.14        73.64        14.37 
TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES 
       48.10        39.32        77.19        98.99        61.58        72.00 
TCGA-A2-A0T3 TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A7-A3IY TCGA-AC-A23C TCGA-AC-A23E 
       49.84        22.45        16.47        11.34        19.23        22.95 
TCGA-AC-A2B8 TCGA-AC-A2FG TCGA-AO-A03V TCGA-AO-A12A TCGA-AO-A1KO TCGA-AO-A1KP 
       22.26        60.92        44.42       102.31        20.45        97.08 
TCGA-AQ-A1H3 TCGA-AR-A0TY TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AT TCGA-AR-A1AU 
       32.52        55.86       103.86        97.68        41.82        94.29 
TCGA-AR-A1AW TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24U TCGA-AR-A24X 
       86.53        94.22       118.59         2.76       102.84        98.76 
TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0WS TCGA-B6-A1KI TCGA-B6-A1KN TCGA-BH-A0B7 
       93.30        71.05        97.48        73.51       139.17        84.13 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C3 TCGA-BH-A0DE 
       75.48        74.14        76.60        77.75        89.06        77.98 
TCGA-BH-A0DT TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18N 
       79.00        63.39        53.26        32.91        35.93        37.74 
TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1FE TCGA-BH-A1FL 
       42.28        49.58        25.81        31.53        74.73        55.00 
TCGA-BH-A1FR TCGA-BH-A202 TCGA-C8-A12Q TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HG 
       53.98        26.14        12.66        12.59        12.33        11.34 
TCGA-C8-A1HI TCGA-D8-A141 TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JJ 
       11.28        20.58        55.50        18.90        14.01        20.09 
TCGA-D8-A1JP TCGA-D8-A1X7 TCGA-D8-A1XD TCGA-D8-A1XO TCGA-D8-A1XS TCGA-D8-A1XY 
       21.01        16.73        17.16        55.30        16.31        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15I TCGA-E2-A15M 
       15.52         9.93        19.43        17.29        55.63        11.05 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IK 
       32.35        28.50        77.65        70.36        33.73        59.18 
TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LS 
        3.88        60.99        11.08        54.18        19.66        52.73 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R5 TCGA-E9-A1R7 
       35.77        35.24        25.84        18.94         3.02        48.23 
TCGA-E9-A1RA TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 
       45.01         6.58        21.27        47.64        32.05        37.74 
TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-EW-A1IX TCGA-EW-A1IY 
       38.37        38.99         7.13        24.56        39.72         8.48 
TCGA-EW-A1J2 TCGA-EW-A1OY TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PD TCGA-EW-A1PG 
       13.25        29.85        39.78        30.08        13.94        34.55 
TCGA-EW-A2FW 
       22.09 

$subtype5
TCGA-A7-A26I TCGA-A7-A2KD TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AR-A1AR TCGA-AR-A2LR 
       21.73        22.32        16.57        13.71        17.23        57.27 
TCGA-LL-A5YP TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT 
       14.79        87.25        99.12        19.20        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0DA TCGA-A7-A13D 
       29.98        47.31        50.83        24.39        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV 
       20.19        23.74        14.50        21.17        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
        9.37         8.75        73.05        13.58         0.03         1.12 
TCGA-AN-A0AT TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A1AH 
        0.33        60.56        61.87        82.62        84.10       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24S 
      108.36       101.00        99.32        33.73       104.28        97.84 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF 
       99.62        85.64        93.83        10.59        77.62       101.52 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
       37.87         7.07        74.99        61.51        74.89        77.95 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1F6 TCGA-BH-A1FN 
       81.73        78.28        37.55        51.16        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A130 
       55.50       130.16        18.64        11.93        12.66        12.16 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM 
       13.51        12.59        12.92        10.92         0.16        12.33 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A143 TCGA-D8-A147 
        0.03         9.76        14.43        13.02        14.17        19.20 
TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ 
       15.78        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-A15K TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1L7 
       25.05         9.04        76.57        53.62        33.70        60.36 
TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 
       24.59       106.75       102.61         8.75        34.92        38.76 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1RH 
       17.69        22.29        34.16        36.20        41.62        46.59 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1OW 
       40.73         0.69         1.94        30.18        18.21        22.82 
TCGA-EW-A1P4 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-EW-A6SD 
       29.82        19.99         6.15        17.49        24.99        33.21 
TCGA-GI-A2C9 TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y 
      109.87        69.30         2.60        14.47        16.08        15.68 
TCGA-LL-A7SZ TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO 
       19.53        36.36        20.38        23.47        14.07        28.21 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
        9.93        20.68        19.27        17.26 

$subtype6
TCGA-A2-A25A TCGA-A7-A26H TCGA-A7-A3J1 TCGA-AC-A3W6 TCGA-AQ-A7U7 TCGA-AR-A1AM 
      107.70        23.80        11.28        19.79        19.20        98.33 
TCGA-AR-A2LL TCGA-BH-A0B6 TCGA-E2-A2P5 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U 
       66.15        81.63        26.99        75.02        85.35        13.22 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0EP TCGA-A2-A1FX TCGA-A2-A1G0 
      136.73       114.81       107.93       118.45        60.72        20.25 
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-A7-A13H TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FK 
       29.56        99.35        40.57        86.66        90.71        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        74.14        19.33        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3YI TCGA-AC-A6IV TCGA-AC-A6IX 
       22.19        24.13        25.05        23.24        18.67        12.26 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        86.53        63.62        38.17        39.39        40.54 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0W7 TCGA-BH-A1EW 
      170.17        85.35        14.30        81.83        44.81        55.69 
TCGA-BH-A203 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A8G0 TCGA-C8-A26W 
       38.60        36.82        36.79        20.12        21.76        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A3M7 TCGA-C8-A8HQ TCGA-C8-A8HR 
       12.36        12.95        16.87        33.99        12.49        13.41 
TCGA-D8-A145 TCGA-D8-A1X9 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       13.48        23.90        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        17.06         1.61        10.09        13.08        12.26 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A14U TCGA-E2-A15P TCGA-E2-A1LE TCGA-E2-A2P6 
       16.18        12.66        43.33        19.56        28.90        34.55 
TCGA-E2-A3DX TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS 
       43.56        24.82        28.27        39.09        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-EW-A1PA TCGA-EW-A2FS TCGA-EW-A2FV TCGA-GI-A2C8 
        9.47        30.44        18.90        52.73        25.91         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       110.50 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A73Z TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-S3-A6ZH 
       11.57         7.10         7.46        40.11        18.48        21.07 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.12     0.16     5.26     2.76     0.03     1.61 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  160.90   110.60   212.25   139.17   130.16   216.76 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  21.515   24.280   31.360   35.930   24.490   30.080 
[1] "1.1 - 160.9 (21.5)" "0.2 - 110.6 (24.3)" "5.3 - 212.2 (31.4)"
[4] "2.8 - 139.2 (35.9)" "0.0 - 130.2 (24.5)" "1.6 - 216.8 (30.1)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      10       12        0        1        49        32         1
  subtype2       4       11        3        1        23        22         0
  subtype3       7        6        1        0        12        20         0
  subtype4      18       11        1        1        46        21         0
  subtype5      11        6        0        1        63        33         0
  subtype6      12        5        0        1        26        34         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         19          2          8        0       1
  subtype2         13          1         12        4       0
  subtype3          9          1          1        1       0
  subtype4         13          3          3        1       1
  subtype5         22          3          3        1       0
  subtype6         16          3         15        1       0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          10        4        7       18       11       12
  STAGE IA         12       11        6       11        6        5
  STAGE IB          0        3        1        1        0        0
  STAGE II          1        1        0        1        1        1
  STAGE IIA        49       23       12       46       63       26
  STAGE IIB        32       22       20       21       33       34
  STAGE III         1        0        0        0        0        1
  STAGE IIIA       19       13        9       13       22       16
  STAGE IIIB        2        1        1        3        3        3
  STAGE IIIC        8       12        1        3        3       15
  STAGE IV          0        4        1        1        1        1
  STAGE X           1        0        0        1        0        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  32  79  20   3
  subtype2  23  50  18   3
  subtype3  21  28   9   1
  subtype4  54  57   6   4
  subtype5  25 104  11   5
  subtype6  29  61  21   3
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       32       23       21       54       25       29
  T2       79       50       28       57      104       61
  T3       20       18        9        6       11       21
  T4        3        3        1        4        5        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 65 43 14  8
  subtype2 41 31  7 13
  subtype3 27 25  6  1
  subtype4 61 45 10  4
  subtype5 82 39 21  3
  subtype6 42 46  9 16
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       65       41       27       61       82       42
  N1       43       31       25       45       39       46
  N2       14        7        6       10       21        9
  N3        8       13        1        4        3       16
[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"
D11V6, binary
          cls
clus         0   1
  subtype1 114   0
  subtype2  52   4
  subtype3  45   1
  subtype4 101   1
  subtype5 115   1
  subtype6  89   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  114    0
  subtype2   52    4
  subtype3   45    1
  subtype4  101    1
  subtype5  115    1
  subtype6   89    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      114       52       45      101      115       89
  1        0        4        1        1        1        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"
D11V7, binary
          cls
clus         0   1
  subtype1 132   3
  subtype2  92   2
  subtype3  59   0
  subtype4 119   2
  subtype5 143   2
  subtype6 114   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  132    3
  subtype2   92    2
  subtype3   59    0
  subtype4  119    2
  subtype5  143    2
  subtype6  114    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      132       92       59      119      143      114
  MALE          3        2        0        2        2        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"
D11V8, binary
          cls
clus        0  1
  subtype1 70 54
  subtype2 40 50
  subtype3 19 33
  subtype4 47 63
  subtype5 57 74
  subtype6 49 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70   54
  subtype2   40   50
  subtype3   19   33
  subtype4   47   63
  subtype5   57   74
  subtype6   49   63
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        70       40       19       47       57       49
  YES       54       50       33       63       74       63
[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                            96
  subtype2                          0                            34
  subtype3                          0                            36
  subtype4                          0                            94
  subtype5                          1                           128
  subtype6                          0                            48
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             17                   0
  subtype2                             55                   0
  subtype3                             14                   0
  subtype4                             15                   0
  subtype5                              2                   5
  subtype6                             58                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                5
  subtype2                     2                                1
  subtype3                     3                                1
  subtype4                     0                                6
  subtype5                     4                                2
  subtype6                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                  9              8
  subtype2                  1              1
  subtype3                  0              5
  subtype4                  1              5
  subtype5                  0              3
  subtype6                  4              3
D11V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA          96       34       36       94      128
  INFILTRATING LOBULAR CARCINOMA         17       55       14       15        2
  MEDULLARY CARCINOMA                     0        0        0        0        5
  METAPLASTIC CARCINOMA                   0        2        3        0        4
  MIXED HISTOLOGY (PLEASE SPECIFY)        5        1        1        6        2
  MUCINOUS CARCINOMA                      9        1        0        1        0
  OTHER, SPECIFY                          8        1        5        5        3
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          48
  INFILTRATING LOBULAR CARCINOMA         58
  MEDULLARY CARCINOMA                     0
  METAPLASTIC CARCINOMA                   0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      4
  OTHER, SPECIFY                          3
[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"
D11V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    15                        25    95
  subtype2     1                        36    55
  subtype3     2                         8    48
  subtype4     8                         3   110
  subtype5    15                        56    72
  subtype6    10                        17    86
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           15        1        2        8       15
  BLACK OR AFRICAN AMERICAN       25       36        8        3       56
  WHITE                           95       55       48      110       72
                           clus
vv                          subtype6
  ASIAN                           10
  BLACK OR AFRICAN AMERICAN       17
  WHITE                           86
[1] 3 6
[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   6 125
  subtype2   4  83
  subtype3   3  53
  subtype4   7 107
  subtype5   3 135
  subtype6   6 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  125
  subtype2    4   83
  subtype3    3   53
  subtype4    7  107
  subtype5    3  135
  subtype6    6  105
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        4        3        7        3        6
  NOT HISPANIC OR LATINO      125       83       53      107      135      105
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 265  49
  subtype2 212  21
  subtype3 101  16
subtype1 subtype2 subtype3 
     314      233      117 
subtype1 subtype2 subtype3 
      49       21       16 
$subtype1
TCGA-A2-A1G4 TCGA-A7-A13G TCGA-A7-A26I TCGA-AC-A62X TCGA-AR-A1AR TCGA-AR-A2LR 
       19.56        23.61        21.73        13.71        17.23        57.27 
TCGA-BH-A18H TCGA-BH-A1F5 TCGA-BH-A8FY TCGA-C8-A1HL TCGA-E2-A15O TCGA-EW-A1J5 
       21.44        89.16         9.70        10.42        50.79        15.68 
TCGA-LL-A442 TCGA-LL-A5YP TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-3C-AAAU 
       29.23        14.79        18.87        13.94        52.96       133.05 
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CW TCGA-A2-A0T3 
      131.67         9.96        87.25        99.12       107.93        49.84 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       23.47        17.36        19.20        42.44        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       29.98        32.75        47.31        35.93        50.83        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       23.21        26.96        35.67        31.73        20.19        25.15 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SE 
       23.74        20.61        10.29        13.41        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A23C 
       17.92        12.10        10.29         9.37         8.75        19.23 
TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A3YJ TCGA-AC-A5EH TCGA-AC-A6IW TCGA-AC-A7VB 
        5.72        73.05        24.79        16.80        13.58         8.22 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A0AT TCGA-AO-A03V TCGA-AO-A12F TCGA-AO-A12H 
        1.12         1.32         0.33        44.42        60.56        40.57 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AR-A0TS 
       97.08        61.87        82.62        11.51        15.62        84.10 
TCGA-AR-A0TY TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AO 
       55.86       125.16       108.36       101.00       103.86        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY 
       93.90        99.32        41.82        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 
      102.84        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A1KN 
       85.64        93.83        10.59        77.62       101.52       139.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0B7 
       37.87         7.07        74.99        18.84        62.93        84.13 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       61.51        74.89        75.48        85.87        77.75        77.95 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0H5 TCGA-BH-A0HA 
       89.06        90.97        81.73        78.28        53.26        52.96 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R 
        2.37        16.96        90.84        26.66        37.74        37.55 
TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EW 
       66.05        51.16        69.93       113.82        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM 
       49.58        25.81        97.48        25.08        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A209 
       72.07        53.98        55.50        26.14        83.31       130.16 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       18.64         9.63        11.93        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.16        13.51        12.59        12.59 
TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A278 TCGA-C8-A27A 
       12.03        12.33        12.95        12.33         9.76        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-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       14.17        17.49        15.78        18.90        53.00        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.09        20.12        20.09        12.20        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XK 
       16.73        27.58        12.39        17.16        15.22        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31        16.64        15.16        43.04 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.14        17.42        16.04 
TCGA-D8-A27V TCGA-D8-A73W TCGA-E2-A10A TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       12.53        12.66        40.41        47.15        44.68        40.96 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       38.60        33.17        75.98        32.02        31.96        69.34 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15M 
       63.62        69.96        25.05        12.92         9.04        11.05 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 
       56.94        51.39        76.57        53.62        32.35        28.50 
TCGA-E2-A1IE TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       77.65        33.70        60.36        19.66        24.59        75.81 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61         8.75        52.73        34.92        38.76 
TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE 
       34.82        22.29        34.16        36.20        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       35.24        34.95         6.12        11.15        48.23        45.01 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D 
       46.65        21.27        46.59        42.25        38.37        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A3Q9 
       40.73        40.50         0.69        38.99        24.56        32.91 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ 
       30.18        23.84         0.79        25.81        26.40        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY 
       18.90        16.57        28.77        25.94        22.82        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       40.41        41.13        29.82        18.48        30.08        19.99 
TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A6SA 
        6.15        52.73        25.91        22.09        17.49        16.77 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DM TCGA-GM-A3XL TCGA-HN-A2NL 
       24.99        33.21       109.87       106.06        69.30         2.60 
TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D6 TCGA-OL-A5D8 
       32.75        14.47        16.08        15.68        36.30        31.99 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66P 
       36.36        22.32        20.38        26.70        23.47        14.07 
TCGA-OL-A6VO TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       28.21         0.16         9.93        20.68        19.27        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S 
       17.03         3.81 

$subtype2
TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A2-A25A TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3J1 
       48.56        48.36       107.70        23.80        22.32        11.28 
TCGA-A7-A5ZX TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AQ-A54O 
       11.05        16.57        19.79        14.53        19.33        32.91 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LL TCGA-AR-A5QM TCGA-BH-A0B6 TCGA-BH-A0DO 
       19.20        98.33        66.15        73.35        81.63        54.05 
TCGA-E2-A2P5 TCGA-E2-A572 TCGA-GM-A2DD TCGA-GM-A2DO TCGA-LD-A74U TCGA-LL-A440 
       26.99        39.72        75.02        85.35        13.22        24.95 
TCGA-LL-A50Y TCGA-LL-A740 TCGA-OL-A5RU TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-3C-AALJ 
       25.05        14.50        40.08        11.41       108.07        48.46 
TCGA-3C-AALK TCGA-4H-AAAK TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0EP 
       47.61        11.44       136.73       114.81       107.93       118.45 
TCGA-A2-A1FX TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ 
       60.72        18.15        36.23        39.65        56.28        50.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A13H TCGA-A7-A3IZ 
        7.30        21.30        21.14        21.90        29.56        10.59 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A56D TCGA-A7-A5ZW 
       14.70        14.93        13.74        14.66        14.73        10.72 
TCGA-A7-A6VX TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FK 
       10.42        73.91        99.35        40.57        86.66        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       15.48        23.24        29.26        14.96        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OS 
       18.67        12.26         1.68         0.03        20.19         2.30 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       40.54        33.30        38.96       170.17        85.35        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0E2 TCGA-BH-A203 TCGA-BH-A28O TCGA-BH-A28Q 
      103.63        71.15        14.30        38.60        36.82        36.79 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R9 
       20.12        10.52       110.60        20.88        23.51         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        12.46        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        15.45        16.87        16.70         0.03 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Z 
       33.99        12.95        13.02        12.49        13.41        20.88 
TCGA-D8-A1X9 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       23.90        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.48        17.06         1.61        10.09        13.08        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A14U 
       33.37        18.51        21.67        16.18        25.22        43.33 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A1LE TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       20.71        21.63        28.90        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1RD 
       30.61        34.29        17.69        24.82        28.27         1.12 
TCGA-E9-A226 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       34.45        39.09         1.94        12.33        29.72         9.47 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1PA TCGA-EW-A2FR TCGA-EW-A3E8 
       30.44        26.70        27.85        18.90        55.00        34.03 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        15.22        31.30         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      115.69       101.62       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YM 
       21.24         7.10        13.28        10.62        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.70        22.26         2.63         7.46        19.53        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RV 
       17.49        27.91        22.39         2.10        58.62        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       28.87        24.72        65.62        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-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       66.84        29.03        15.35        16.04       107.05 

$subtype3
TCGA-A7-A26E TCGA-AO-A1KT TCGA-D8-A146 TCGA-E2-A1BC TCGA-E2-A1L8 TCGA-A1-A0SB 
       31.36        17.79        21.14        16.47        73.64         8.52 
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CS 
       14.37        48.10        20.88        39.32       101.98        77.19 
TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       98.99        61.58        72.00        22.45        20.25        16.47 
TCGA-A7-A0DB TCGA-A7-A3IY TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG 
       33.11        11.34        22.95        22.26        90.71        60.92 
TCGA-AC-A3EH TCGA-AO-A12A TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AR-A1AL TCGA-AR-A1AN 
        6.48       102.31        20.45        32.52        97.68        96.00 
TCGA-AR-A1AU TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24V TCGA-AR-A255 
       94.29       120.33        99.78         2.76       105.30        71.05 
TCGA-B6-A0IH TCGA-B6-A0RH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 
      112.37       212.25        97.48        73.51        63.09        81.44 
TCGA-BH-A0B5 TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       70.22        74.14        76.60        77.98        67.10        29.98 
TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0W7 
       79.00        70.88        81.83        63.32        63.39        44.81 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EY 
       32.91        35.93        72.56        91.99        42.28        17.69 
TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A208 
       31.53       120.62        74.73        33.99        28.14        57.83 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A138 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A1JB 
       11.77        12.66        12.49        20.58        13.48        55.50 
TCGA-D8-A1JD TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XB TCGA-D8-A1XO 
       18.15        14.01        21.01        14.70        18.15        55.30 
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-A15I TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.29        18.21        55.63        19.56        87.22        33.01 
TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.25        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E9-A1NG TCGA-E9-A1NH 
       22.19        60.99        11.08        54.18        25.84        18.94 
TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 
        3.02        40.24         6.58        47.64        32.05        37.74 
TCGA-E9-A22E TCGA-E9-A249 TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J2 
       41.72         7.13        12.20        39.72         8.48        13.25 
TCGA-EW-A1P1 TCGA-EW-A1PD TCGA-EW-A1PG 
       39.78        13.94        34.55 

subtype1 subtype2 subtype3 
    0.16     0.03     2.76 
subtype1 subtype2 subtype3 
  160.90   216.76   212.25 
subtype1 subtype2 subtype3 
  27.895   22.390   34.550 
[1] "0.2 - 160.9 (27.9)" "0.0 - 216.8 (22.4)" "2.8 - 212.2 (34.5)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      25       22        2        3       126        74         0
  subtype2      17       18        3        2        59        60         2
  subtype3      20       11        0        0        34        28         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         45          7          8        3       1
  subtype2         33          5         30        3       0
  subtype3         14          1          4        2       1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          25       17       20
  STAGE IA         22       18       11
  STAGE IB          2        3        0
  STAGE II          3        2        0
  STAGE IIA       126       59       34
  STAGE IIB        74       60       28
  STAGE III         0        2        0
  STAGE IIIA       45       33       14
  STAGE IIIB        7        5        1
  STAGE IIIC        8       30        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  76 199  31  11
  subtype2  60 122  46   5
  subtype3  48  58   8   3
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       76       60       48
  T2      199      122       58
  T3       31       46        8
  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 163 106  35   9
  subtype2 100  76  23  31
  subtype3  55  47   9   5
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      163      100       55
  N1      106       76       47
  N2       35       23        9
  N3        9       31        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 257   3
  subtype2 161   3
  subtype3  98   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  257    3
  subtype2  161    3
  subtype3   98    2
   clus
vv  subtype1 subtype2 subtype3
  0      257      161       98
  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 312   6
  subtype2 231   2
  subtype3 116   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  312    6
  subtype2  231    2
  subtype3  116    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      312      231      116
  MALE          6        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
          cls
clus         0   1
  subtype1 139 152
  subtype2 102 123
  subtype3  41  62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139  152
  subtype2  102  123
  subtype3   41   62
     clus
vv    subtype1 subtype2 subtype3
  NO       139      102       41
  YES      152      123       62
[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                           257
  subtype2                          0                            91
  subtype3                          0                            88
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             15                   5
  subtype2                            127                   0
  subtype3                             19                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     4                                9
  subtype2                     5                                2
  subtype3                     0                                5
          vv
clus       MUCINOUS CARCINOMA OTHER, SPECIFY
  subtype1                 11             16
  subtype2                  3              5
  subtype3                  1              4
D12V9, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         257       91       88
  INFILTRATING LOBULAR CARCINOMA         15      127       19
  MEDULLARY CARCINOMA                     5        0        0
  METAPLASTIC CARCINOMA                   4        5        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        9        2        5
  MUCINOUS CARCINOMA                     11        3        1
  OTHER, SPECIFY                         16        5        4
[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    26                        80   210
  subtype2    18                        59   153
  subtype3     7                         6   103
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           26       18        7
  BLACK OR AFRICAN AMERICAN       80       59        6
  WHITE                          210      153      103
[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  14 289
  subtype2   9 214
  subtype3   6 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  289
  subtype2    9  214
  subtype3    6  105
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           14        9        6
  NOT HISPANIC OR LATINO      289      214      105
[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"
