[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/15076769/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/15246568/BRCA-TP.mergedcluster.txt"

nPatients in clinical file=1080, in cluster file=1098, common to both=1080
[1]   12 1080
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
102 156 118  92  58 
  1   2   3   4   5 
102 156 118  92  58 
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
271 400  97 251  43 
  1   2   3   4   5 
271 400  97 251  43 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5   6 
153 111 177 128 127  54 
  1   2   3   4   5   6 
153 111 177 128 127  54 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
153 137 120 
  1   2   3 
153 137 120 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 64  49  93  54 118  32 
  1   2   3   4   5   6 
 64  49  93  54 118  32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
558 305 213 
  1   2   3 
558 305 213 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
291 163  90 289 184  59 
  1   2   3   4   5   6 
291 163  90 289 184  59 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
302 207 270 281 
  1   2   3   4 
302 207 270 281 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
297 151 244 139  97 132 
  1   2   3   4   5   6 
297 151 244 139  97 132 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
181 136  99 109 125 
  1   2   3   4   5 
181 136  99 109 125 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
303 237 110 
  1   2   3 
303 237 110 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 1080 columns.

[1] "Batch" "20"   
[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=130,	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=728,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'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"
            315     412    
freq.values "1"     "1"    
freq >=3    "FALSE" "FALSE"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=44,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 1080 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "NUMBER_OF_LYMPH_NODES"                 
[10] "RACE"                                  
[11] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=65, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
279 626 131  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
279 626 131  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
279 626 131  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
279 626 131  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
511 356 118  75 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
511 356 118  75 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
511 356 118  75 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
511 356 118  75 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=31, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 17  3
  subtype2 36  3
  subtype3 97 19
  subtype4 87 13
  subtype5 96 12
  subtype6 56 15
  subtype7 16  3
  subtype8 32  7
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      20       39      116      100      108       71       19       39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       3        3       19       13       12       15        3        7 
$subtype1
TCGA-A1-A0SD TCGA-A1-A0SH TCGA-A1-A0SM TCGA-A2-A0SV TCGA-A8-A06P TCGA-A8-A07G 
       14.37        47.24         7.96        27.12        13.02        18.97 
TCGA-A8-A07I TCGA-A8-A08Z TCGA-A8-A097 TCGA-AN-A03X TCGA-AN-A0AS TCGA-AN-A0XN 
       14.01        40.01        12.00         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-BH-A0DZ TCGA-BH-A0H6 TCGA-BH-A18J TCGA-BH-A1EO TCGA-C8-A12O 
        5.59        16.27        24.56        20.12        91.99        12.66 
TCGA-D8-A141 TCGA-E2-A153 
       20.58        23.24 

$subtype2
TCGA-A1-A0SE TCGA-A2-A0CP TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES 
       43.43        92.48        98.99        53.13        80.28        72.00 
TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0T7 TCGA-A2-A0YL TCGA-A8-A08O TCGA-A8-A09A 
       24.72        54.64        20.75        48.46        31.00         9.99 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0JA TCGA-AO-A0JB 
       13.02        21.04        80.28        61.35        21.53        50.70 
TCGA-AO-A12C TCGA-AO-A12E TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AU TCGA-B6-A0IE 
       65.56        57.30        43.73        43.56        76.21        65.72 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0DG 
      140.48       157.41       113.79        28.50        37.74        23.44 
TCGA-BH-A0DI TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-C8-A132 TCGA-C8-A1HI TCGA-E2-A14Q 
       22.13        46.19        24.43         1.87        11.28        38.24 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A1B1 
       20.71        12.92        53.03 

$subtype3
TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68       121.94        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0T3 
      107.93        25.22        74.40        35.05        34.29        49.84 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F 
       21.67        23.77        38.30        30.61        37.45        25.15 
TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L 
       13.02        29.03        31.00         1.02         9.01        32.05 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
       10.98         9.99        45.07        18.05        36.95        13.02 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
       33.01        19.96        33.01        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       33.07        25.02         8.98         0.23         0.62         2.96 
TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.36         6.44         5.65         0.36         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 
        0.33        95.70        68.75        47.87        29.13        21.40 
TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A126 TCGA-AO-A12H TCGA-AQ-A04H TCGA-AR-A0TQ 
       20.32        50.24       108.72        28.37        24.79        73.64 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-B6-A0IM 
       42.35        98.93        55.86       107.24        83.87       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT 
       84.59       110.14        68.45        81.17        78.02       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X5 TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0B8 
       79.63        18.35        68.94        24.53        39.16        51.58 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0E2 TCGA-BH-A0GZ 
       42.90        45.83        38.01        13.91        14.30        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX 
       15.16        37.78        23.08        26.50        51.32        27.25 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U 
       26.66        37.74        37.55       113.82        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A1HG TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 
       12.66        12.66        11.34         3.25        13.25        43.00 
TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       59.41        46.59        40.41        44.68        33.17        33.30 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       32.02        21.04        23.34        21.63        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        14.99 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       31.79        28.01        19.20        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST 
       87.25        24.79        55.00        67.33        33.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O 
       35.31        35.67        31.73        20.19        33.99         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-AN-A04D TCGA-AN-A0AL 
        8.98        24.99         0.99        43.00         1.71         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX 
        0.16         0.33         0.33         7.96         7.59         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL 
        0.53         0.33        58.95        52.18        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TP 
      102.58       106.78       108.03        48.36        26.93       111.32 
TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       74.79        13.71        65.36        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 
       52.77        43.07        17.23        33.73       143.38        32.78 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX 
      176.98       140.88       211.56        89.46       131.21        21.47 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
      186.48        59.84        39.55        51.68        24.85        44.05 
TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA 
       11.67        48.23         4.41         9.63         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1F0 TCGA-C8-A12L 
        2.01        90.84        55.63        51.16        25.81        11.93 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A143 
       12.66         2.24         1.12        11.90        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       19.20        47.15        38.60        31.96        28.60        25.41 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B5 
       14.79        25.05        60.53        32.35 

$subtype5
TCGA-A2-A04N TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EV 
      104.81        88.60        75.55        61.58       101.72        31.82 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A7-A0CH 
       17.46        32.55        25.28        50.47        49.48        35.47 
TCGA-A7-A0DB TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07S TCGA-A8-A08A 
       33.11        53.06        26.01        18.97         7.99         0.99 
TCGA-A8-A08C TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       28.96        33.01       112.08        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 
       12.00         1.02        19.04        15.02        12.00        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0FK 
       27.02        17.03        38.04         0.33         0.33         7.00 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A0J8 TCGA-AO-A125 
       12.33         0.30         0.33         5.33        22.36        99.25 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12G TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AP 
       90.58        98.27        41.62         5.26        51.25        39.98 
TCGA-AR-A1AS TCGA-AR-A1AW TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       37.81        63.62       149.59       220.90       129.57        50.70 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WZ 
      110.93       234.28       172.96       162.05       102.77       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
      129.70        28.27        48.36        37.22        32.02        18.21 
TCGA-BH-A0BJ TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0DO 
       21.70        27.19        53.95        45.57        49.94        17.26 
TCGA-BH-A0DP TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.65        38.47        15.68        44.81        32.58        24.49 
TCGA-BH-A0HA TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        23.90        20.38         2.50        13.61        36.85 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18S 
       23.93        24.95        42.35         7.23        72.56        66.05 
TCGA-BH-A1ET TCGA-C8-A12N TCGA-D8-A146 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       82.85        11.77        21.14        37.51        28.44        28.87 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I 
       19.43        23.87        22.82        17.29        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B4 TCGA-E2-A1BD 
       19.40         9.04        20.58        19.56        33.01        17.10 

$subtype6
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EY TCGA-A2-A0SW 
      101.98        55.43        56.81        34.55        63.29        44.88 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A076 
       17.13        21.90         1.02        17.98        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A092 
       43.00        15.06        38.01        37.05         9.99        30.97 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X TCGA-AN-A04C TCGA-AN-A0FT 
       45.07         1.02         0.99        14.01         1.78         7.04 
TCGA-AN-A0FV TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM 
        0.33        66.77        32.78        72.00        76.77        71.80 
TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 TCGA-AR-A1AT TCGA-B6-A0I8 
       64.04       130.09        64.83       114.02        41.82        24.62 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH TCGA-B6-A0RS TCGA-BH-A0AW 
       12.13       146.50        18.77       189.01       100.70        20.45 
TCGA-BH-A0B7 TCGA-BH-A0BR TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0EE TCGA-BH-A0GY 
       56.98        53.69        44.02         2.56        31.00        30.35 
TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U 
       41.00        12.89        50.79        30.28         7.36        51.39 
TCGA-BH-A1EV TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A135 
       12.00        11.77        12.66         0.39         3.16         1.05 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HL TCGA-D8-A13Z TCGA-E2-A107 
        4.11         4.08        10.92        10.42        20.88        34.42 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A1B0 
       40.11        40.96        34.26        27.12        53.62 

$subtype7
TCGA-A2-A0CL TCGA-A2-A0EQ TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A0A7 TCGA-AN-A0AJ 
       99.12        79.76        12.00        31.00         0.99         9.96 
TCGA-AO-A03O TCGA-AO-A0JC TCGA-AR-A0TT TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0WS 
       81.63        50.86        86.66        61.28        62.14        97.48 
TCGA-BH-A0BF TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0H5 TCGA-BH-A0W7 TCGA-C8-A1HM 
       25.71        49.05        41.75        35.51        44.81         2.30 
TCGA-E2-A14Z 
       18.51 

$subtype8
TCGA-A2-A0EN TCGA-A2-A0EW TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0YK 
      134.40        61.94        44.28        20.52        18.90        19.33 
TCGA-A7-A0CG TCGA-A8-A07E TCGA-A8-A07J TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
       34.29        19.99        12.00         7.17         6.28         0.33 
TCGA-AN-A0XS TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
        0.33        26.04        53.03        21.37        26.24        62.04 
TCGA-AR-A1AL TCGA-B6-A0IH TCGA-B6-A0X7 TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0BM 
       48.82       112.37        58.88        25.55        46.95        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DQ TCGA-BH-A0DX 
       35.67        48.69        48.13        31.17         3.22        47.41 
TCGA-BH-A0HK TCGA-BH-A18F TCGA-BH-A1EU TCGA-BH-A1EW TCGA-D8-A145 TCGA-E2-A108 
        5.85         8.81        42.28        55.69        13.48        27.52 
TCGA-E2-A15M TCGA-E2-A1B6 TCGA-E2-A1BC 
       11.05        28.50        16.47 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.33     1.87     0.23     0.16     0.30     0.33     0.99     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   91.99   157.41   188.68   211.56   234.28   189.01    99.12   134.40 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  15.320   43.730   30.805   31.875   28.655   31.000   44.810   27.520 
[1] "0.3 - 92.0 (15.3)"  "1.9 - 157.4 (43.7)" "0.2 - 188.7 (30.8)"
[4] "0.2 - 211.6 (31.9)" "0.3 - 234.3 (28.7)" "0.3 - 189.0 (31.0)"
[7] "1.0 - 99.1 (44.8)"  "0.3 - 134.4 (27.5)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        0        0         8         3          5          1
  subtype2       2        2        0        12        10          8          0
  subtype3       8        6        4        35        35         20          6
  subtype4       9        9        0        45        19          9          1
  subtype5      16       12        0        43        15         10          5
  subtype6       4        2        0        21        19         15          2
  subtype7       4        1        0         6         4          4          0
  subtype8       6        1        2        14         6          6          0
          vv
clus       STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          0        2         0       0
  subtype2          2        1         1       1
  subtype3          3        1         0       3
  subtype4          4        3         0       1
  subtype5          2        3         0       4
  subtype6          6        3         0       1
  subtype7          0        0         0       1
  subtype8          2        1         0       2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        2        8        9       16        4        4
  STAGE IA          0        2        6        9       12        2        1
  STAGE IB          0        0        4        0        0        0        0
  STAGE IIA         8       12       35       45       43       21        6
  STAGE IIB         3       10       35       19       15       19        4
  STAGE IIIA        5        8       20        9       10       15        4
  STAGE IIIB        1        0        6        1        5        2        0
  STAGE IIIC        0        2        3        4        2        6        0
  STAGE IV          2        1        1        3        3        3        0
  STAGE TIS         0        1        0        0        0        0        0
  STAGE X           0        1        3        1        4        1        1
            clus
vv           subtype8
  STAGE I           6
  STAGE IA          1
  STAGE IB          2
  STAGE IIA        14
  STAGE IIB         6
  STAGE IIIA        6
  STAGE IIIB        0
  STAGE IIIC        2
  STAGE IV          1
  STAGE TIS         0
  STAGE X           2
[1] 11  8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  6 13  0  2
  subtype2  8 21  9  0
  subtype3 25 75 14  6
  subtype4 23 67  8  2
  subtype5 40 55  9  6
  subtype6 11 49 12  2
  subtype7  7 10  3  0
  subtype8 13 21  4  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        6        8       25       23       40       11        7       13
  T2       13       21       75       67       55       49       10       21
  T3        0        9       14        8        9       12        3        4
  T4        2        0        6        2        6        2        0        2
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1  6  6  7  1
  subtype2 14 16  5  3
  subtype3 49 50 14  4
  subtype4 64 24  8  5
  subtype5 66 31  7  5
  subtype6 24 26 14  8
  subtype7 11  5  3  0
  subtype8 21 12  3  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        6       14       49       64       66       24       11       21
  N1        6       16       50       24       31       26        5       12
  N2        7        5       14        8        7       14        3        3
  N3        1        3        4        5        5        8        0        3
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1  19   2
  subtype2  37   1
  subtype3 115   2
  subtype4  97   3
  subtype5 101   3
  subtype6  70   3
  subtype7  19   0
  subtype8  37   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19    2
  subtype2   37    1
  subtype3  115    2
  subtype4   97    3
  subtype5  101    3
  subtype6   70    3
  subtype7   19    0
  subtype8   37    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  0       19       37      115       97      101       70       19       37
  1        2        1        2        3        3        3        0        1
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  20   1
  subtype2  39   0
  subtype3 117   4
  subtype4 101   0
  subtype5 110   0
  subtype6  74   0
  subtype7  19   1
  subtype8  40   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   39    0
  subtype3  117    4
  subtype4  101    0
  subtype5  110    0
  subtype6   74    0
  subtype7   19    1
  subtype8   40    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       20       39      117      101      110       74       19
  MALE          1        0        4        0        0        0        1
        clus
vv       subtype8
  FEMALE       40
  MALE          0
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            20                              0
  subtype2                            28                              8
  subtype3                           113                              1
  subtype4                            92                              1
  subtype5                            85                             14
  subtype6                            67                              5
  subtype7                            19                              1
  subtype8                            24                             11
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                3
  subtype3                   0                                1
  subtype4                   1                                0
  subtype5                   0                                5
  subtype6                   0                                0
  subtype7                   0                                0
  subtype8                   0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              0
  subtype3                  1              5
  subtype4                  0              6
  subtype5                  1              5
  subtype6                  0              2
  subtype7                  0              0
  subtype8                  0              2
D1V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          20       28      113       92       85
  INFILTRATING LOBULAR CARCINOMA          0        8        1        1       14
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        3        1        0        5
  MUCINOUS CARCINOMA                      0        0        1        0        1
  OTHER  SPECIFY                          1        0        5        6        5
                                  clus
vv                                 subtype6 subtype7 subtype8
  INFILTRATING DUCTAL CARCINOMA          67       19       24
  INFILTRATING LOBULAR CARCINOMA          5        1       11
  MEDULLARY CARCINOMA                     0        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        0        3
  MUCINOUS CARCINOMA                      0        0        0
  OTHER  SPECIFY                          2        0        2
[1] 6 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1  3 18
  subtype2 14 25
  subtype3 35 86
  subtype4 41 60
  subtype5 33 77
  subtype6 22 52
  subtype7  8 12
  subtype8 12 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   18
  subtype2   14   25
  subtype3   35   86
  subtype4   41   60
  subtype5   33   77
  subtype6   22   52
  subtype7    8   12
  subtype8   12   28
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         3       14       35       41       33       22        8       12
  YES       18       25       86       60       77       52       12       28
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         0
  subtype2                                0     4                         3
  subtype3                                0    10                        12
  subtype4                                0     6                        12
  subtype5                                0     2                         5
  subtype6                                1     9                         2
  subtype7                                0     1                         5
  subtype8                                0     0                         1
          vv
clus       WHITE
  subtype1    14
  subtype2    28
  subtype3    74
  subtype4    75
  subtype5    81
  subtype6    43
  subtype7    11
  subtype8    35
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   2        4       10        6        2
  BLACK OR AFRICAN AMERICAN               0        3       12       12        5
  WHITE                                  14       28       74       75       81
                                  clus
vv                                 subtype6 subtype7 subtype8
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   9        1        0
  BLACK OR AFRICAN AMERICAN               2        5        1
  WHITE                                  43       11       35
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus        0  1
  subtype1  0 14
  subtype2  1 32
  subtype3  0 83
  subtype4  1 83
  subtype5  2 70
  subtype6  2 46
  subtype7  1 14
  subtype8  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   14
  subtype2    1   32
  subtype3    0   83
  subtype4    1   83
  subtype5    2   70
  subtype6    2   46
  subtype7    1   14
  subtype8    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        1        2        2
  NOT HISPANIC OR LATINO       14       32       83       83       70       46
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            1        0
  NOT HISPANIC OR LATINO       14       30
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1  82  16
  subtype2 136  19
  subtype3  92  21
  subtype4  79  12
  subtype5  48   7
subtype1 subtype2 subtype3 subtype4 subtype5 
      98      155      113       91       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      16       19       21       12        7 
$subtype1
TCGA-A1-A0SD TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       14.37       121.94        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0YH TCGA-A2-A0YT 
      107.93        25.22        74.40        34.29        21.67        23.77 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A8-A06T TCGA-A8-A06X 
       38.30        30.61        37.45        25.15        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A082 
       26.01         1.02         9.01        32.05        10.98        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A091 
       36.95        13.02        33.01        19.96        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R 
        1.02        50.04        49.05        29.98        33.07         8.98 
TCGA-A8-A0A9 TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0FD 
       27.02         0.33         0.23         0.62         7.36         6.44 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI 
        0.33         0.33         0.33        95.70        21.40        50.24 
TCGA-AQ-A04H TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
       24.79        73.64        42.35        98.93        55.86       107.24 
TCGA-AR-A0U2 TCGA-B6-A0IB TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RI 
       83.87       129.57       126.12       110.14        68.45       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X5 
       81.17        78.02       188.68        79.63        18.35        68.94 
TCGA-BH-A0B4 TCGA-BH-A0B8 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0E2 
       39.16        51.58        42.90        45.83        38.01        14.30 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX 
       10.78        15.16        37.78        26.50        51.32        27.25 
TCGA-BH-A18L TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A1HL 
       26.66       113.82        11.77        12.66        12.66        10.42 
TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14S 
        3.25        13.25        43.00        46.59        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       33.30        32.02        21.04        21.63        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        14.99 

$subtype2
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A0CL TCGA-A2-A0CP 
       43.43        47.24        13.68       104.81        99.12        92.48 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ES 
       98.99        53.13        61.58       134.40        80.28        72.00 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T3 
       31.82        61.94        24.72        54.64        44.28        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YK 
       20.52        17.46        18.90        20.75        25.28        19.33 
TCGA-A2-A0YL TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A8-A07E TCGA-A8-A07J TCGA-A8-A08C 
       48.46        34.29        33.11        19.99        12.00        28.96 
TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A09A TCGA-A8-A0A1 TCGA-A8-A0A2 
       31.00       112.08        40.01         9.99        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
       13.02        21.04        17.03         0.33         0.33         2.96 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XV 
        7.17         6.28         0.36         0.33         0.33         5.33 
TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J9 
       61.35        68.75        47.87        29.13        26.04        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       21.53        50.70        50.86        21.37        26.24        62.04 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AR-A0TT 
      108.72        90.58        65.56        57.30        41.62        86.66 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AU 
       51.25        48.82        43.73        43.56        39.98        76.21 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IH 
       61.28        62.14       149.59       220.90        65.72       112.37 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WS 
       84.59       110.93       172.96       140.48       157.41        97.48 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      113.79       129.70        58.88        24.53        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       46.95        48.36        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BT 
       21.70        61.68        35.67        48.69        27.19        45.57 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       48.13        31.17        23.44        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E1 
       15.65         3.22         2.56        38.47        47.41        15.68 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HF 
       46.19        32.58        24.43        35.51        52.96        23.90 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
        5.85        13.61        36.85        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
        8.81         7.23        72.56        91.99        82.85        42.28 
TCGA-BH-A1EW TCGA-C8-A132 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-D8-A141 TCGA-D8-A145 
       55.69         1.87        11.34        11.28        20.58        13.48 
TCGA-D8-A146 TCGA-E2-A106 TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14Z 
       21.14        59.41        27.52        28.87        38.24        18.51 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        20.71        12.92        17.42        19.40 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC 
       11.05        19.56        53.03        28.50        16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0CY 
       31.79         7.96       101.98        55.43        56.81        55.00 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T1 
       34.55        79.76        63.29        27.12        44.88        17.13 
TCGA-A2-A0YG TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 
       21.90        13.02         1.02        17.98        29.03        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07W 
       53.98        43.00        18.97        18.97        14.01         9.99 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
       15.06        38.01        12.00        37.05         9.99        31.00 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N 
       43.00        30.97        41.98        12.00        45.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04C TCGA-AN-A0AJ 
       25.02         0.99        14.01         0.99         1.78         9.96 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        0.16         0.33         7.04         0.33         0.33        12.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0JD 
        5.59        80.28        66.77        81.63        32.78        72.00 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 
       76.77        71.80        64.04       130.09        64.83       114.02 
TCGA-AR-A1AT TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH 
       41.82        24.62        12.13       146.50        18.77       189.01 
TCGA-B6-A0RO TCGA-B6-A0RS TCGA-BH-A0AW TCGA-BH-A0B1 TCGA-BH-A0B7 TCGA-BH-A0BR 
      162.05       100.70        20.45        37.74        56.98        53.69 
TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0EE 
       53.95        49.05        41.75        44.02        16.27        31.00 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J 
       30.35        23.08        41.00        12.89        50.79        20.12 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EV TCGA-C8-A12L 
       30.28        37.55         7.36        51.39        12.00        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 
       12.66        11.77        12.66        12.66         0.39         3.16 
TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM 
        2.24         1.05         4.11         4.08        10.92         2.30 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14P 
       11.90        20.88        14.17        34.42        40.11        40.96 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1B0 
       34.26        27.12        25.05        23.34        53.62 

$subtype4
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       28.01        19.20        18.02        78.41        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 
       24.79        67.33        33.76        99.19        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE TCGA-A7-A0DA 
        8.38        18.21        18.61        31.73        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
       31.73        20.19        33.99         9.99         8.98        24.99 
TCGA-A8-A08R TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        0.99         1.71         6.51         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       102.58       106.78       108.03        48.36 
TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       26.93       111.32        74.79        13.71        65.36        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       75.55        61.84        52.77        43.07        17.23        33.73 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT 
      143.38        32.78       176.98       140.88       211.56        89.46 
TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 
      131.21        21.47       186.48        59.84        39.55        51.68 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 
       24.85        44.05        11.67        48.23         4.41         9.63 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V 
        5.59        23.05         2.01        90.84        55.63        51.16 
TCGA-BH-A1F0 TCGA-C8-A12V TCGA-C8-A134 TCGA-D8-A142 TCGA-D8-A147 TCGA-E2-A14N 
       25.81        12.66         1.12        13.97        19.20        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A1AZ 
       38.60        31.96        28.60        25.41        14.79        60.53 
TCGA-E2-A1B5 
       32.35 

$subtype5
TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0EM TCGA-A2-A0ET TCGA-A2-A0YC TCGA-A2-A0YF 
       88.60        75.55       101.72        35.05        32.55        50.47 
TCGA-A2-A0YI TCGA-A7-A0CH TCGA-A8-A06P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A08A 
       49.48        35.47        13.02         7.99        45.07         0.99 
TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0AD 
       17.95         9.99        12.00        19.04        15.02        38.04 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A0J8 
        5.65         7.00         0.30         0.33        20.32        22.36 
TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AW 
       99.25        98.27        28.37         5.26        37.81        63.62 
TCGA-B6-A0IC TCGA-B6-A0RP TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-BH-A0BV TCGA-BH-A0E7 
       50.70       102.77       129.57        28.27        49.94        44.81 
TCGA-BH-A0EB TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0W3 TCGA-BH-A18N 
       24.49        24.56        20.38         2.50        23.93        37.74 
TCGA-BH-A18S TCGA-C8-A12N TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 
       66.05        11.77        40.41        37.51        28.44        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15G TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A1B4 
       19.43        23.87        18.21         9.04        20.58        33.01 
TCGA-E2-A1BD 
       17.10 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.33     0.16     0.33     0.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
  234.28   220.90   189.01   211.56   129.57 
subtype1 subtype2 subtype3 subtype4 subtype5 
  32.035   33.110   25.050   32.780   24.560 
[1] "0.2 - 234.3 (32.0)" "0.3 - 220.9 (33.1)" "0.2 - 189.0 (25.1)"
[4] "0.3 - 211.6 (32.8)" "0.3 - 129.6 (24.6)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       6        5        2        32        30         16          5
  subtype2      21       11        4        56        24         23          1
  subtype3       6        4        0        36        27         24          5
  subtype4       9        8        0        40        18          8          1
  subtype5       8        5        0        20        12          6          3
          vv
clus       STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          2        1         0       3
  subtype2          6        3         1       5
  subtype3          8        6         0       1
  subtype4          3        3         0       1
  subtype5          0        1         0       3
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       21        6        9        8
  STAGE IA          5       11        4        8        5
  STAGE IB          2        4        0        0        0
  STAGE IIA        32       56       36       40       20
  STAGE IIB        30       24       27       18       12
  STAGE IIIA       16       23       24        8        6
  STAGE IIIB        5        1        5        1        3
  STAGE IIIC        2        6        8        3        0
  STAGE IV          1        3        6        3        1
  STAGE TIS         0        1        0        0        0
  STAGE X           3        5        1        1        3
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 19 63 14  5
  subtype2 54 79 19  3
  subtype3 18 78 15  7
  subtype4 22 60  8  1
  subtype5 20 31  3  4
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       19       54       18       22       20
  T2       63       79       78       60       31
  T3       14       19       15        8        3
  T4        5        3        7        1        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 44 43  9  4
  subtype2 81 47 15  9
  subtype3 41 39 25 10
  subtype4 58 23  7  4
  subtype5 31 18  5  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       44       81       41       58       31
  N1       43       47       39       23       18
  N2        9       15       25        7        5
  N3        4        9       10        4        2
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1  96   2
  subtype2 146   3
  subtype3 111   6
  subtype4  88   3
  subtype5  54   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96    2
  subtype2  146    3
  subtype3  111    6
  subtype4   88    3
  subtype5   54    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       96      146      111       88       54
  1        2        3        6        3        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus         0   1
  subtype1  98   4
  subtype2 155   1
  subtype3 117   1
  subtype4  92   0
  subtype5  58   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98    4
  subtype2  155    1
  subtype3  117    1
  subtype4   92    0
  subtype5   58    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       98      155      117       92       58
  MALE          4        1        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            97                              1
  subtype2                           113                             29
  subtype3                           110                              6
  subtype4                            84                              1
  subtype5                            44                              4
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                7
  subtype3                   0                                0
  subtype4                   1                                0
  subtype5                   0                                5
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  1              3
  subtype2                  0              7
  subtype3                  0              2
  subtype4                  0              5
  subtype5                  1              4
D2V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          97      113      110       84       44
  INFILTRATING LOBULAR CARCINOMA          1       29        6        1        4
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        7        0        0        5
  MUCINOUS CARCINOMA                      1        0        0        0        1
  OTHER  SPECIFY                          3        7        2        5        4
[1] 6 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus         0   1
  subtype1  28  74
  subtype2  46 110
  subtype3  29  89
  subtype4  40  52
  subtype5  25  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   74
  subtype2   46  110
  subtype3   29   89
  subtype4   40   52
  subtype5   25   33
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        28       46       29       40       25
  YES       74      110       89       52       33
[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"
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        10
  subtype2                                0     6                         8
  subtype3                                1    16                         4
  subtype4                                0     3                        12
  subtype5                                0     2                         6
          vv
clus       WHITE
  subtype1    60
  subtype2   128
  subtype3    65
  subtype4    70
  subtype5    38
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   7        6       16        3        2
  BLACK OR AFRICAN AMERICAN              10        8        4       12        6
  WHITE                                  60      128       65       70       38
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
          cls
clus         0   1
  subtype1   0  66
  subtype2   3 119
  subtype3   2  74
  subtype4   1  75
  subtype5   1  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    3  119
  subtype3    2   74
  subtype4    1   75
  subtype5    1   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        3        2        1        1
  NOT HISPANIC OR LATINO       66      119       74       75       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 228  37
  subtype2 350  42
  subtype3  85  11
  subtype4 218  30
  subtype5  35   8
subtype1 subtype2 subtype3 subtype4 subtype5 
     265      392       96      248       43 
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       42       11       30        8 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SJ 
      129.14       131.67        42.81         9.96        14.37        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CT 
        7.96        39.32        18.21       121.94        55.43        75.25 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       25.22        80.28        74.40        35.05        34.29        31.82 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YG 
       27.12        44.88        49.84        20.52        20.75        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25E TCGA-A7-A0CD 
       23.77        17.36        60.72        42.44       105.34        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       30.61        29.79        25.15        20.61        22.32        10.59 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       14.93        13.74        17.92        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       53.06        29.03         1.02        53.98         9.01        43.00 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 
       18.97        14.01        32.05        10.98         9.99        36.95 
TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       13.02        33.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E 
       31.00        33.01        12.00         9.99         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A4 
       45.07        29.98        33.07         8.98         0.99        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V 
       21.04        27.02         5.72        99.35        26.04        11.44 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 
        8.22        20.19         0.33         0.33         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XW 
        2.96         9.96         0.33         0.36         0.33         5.59 
TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 
       80.28        81.63        95.70        47.87        32.78        21.40 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A12E 
       72.00        76.77        26.24        50.24        71.80        57.30 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       61.87         0.53        17.79        24.79         5.65        15.62 
TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AK 
       32.91        73.64       107.24        83.87       114.02        51.25 
TCGA-AR-A1AP TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 
       39.98        94.22        87.22        85.35        79.00        89.00 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 TCGA-B6-A0IG 
       72.76        58.92        54.21        66.15        12.13       146.50 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KN 
       68.45        81.17       162.05        79.63       113.79       139.17 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0C7 
       68.12        24.53        39.16        32.02        18.21        42.90 
TCGA-BH-A0DD TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DZ TCGA-BH-A0E2 
       45.83        22.13        48.23         3.22        16.27        14.30 
TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       24.43        23.08        51.32        27.25        50.79        23.93 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
        7.23        26.66        37.74        37.55        66.05        51.39 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM 
       69.93       113.82        55.69        31.53        24.66        45.63 
TCGA-BH-A201 TCGA-BH-A42T TCGA-BH-A5J0 TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q 
       28.14        10.52        23.51        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HG 
       12.66         0.39         1.87         4.11         4.08        11.34 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       12.03        10.42         3.25         8.28         9.67        12.20 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1J9 
        0.23        12.49        19.46        11.90        13.25        17.49 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X9 
       15.78        18.15        18.90        18.97        13.32        23.90 
TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y0 
       27.58        15.22        16.31         6.35        16.54        15.52 
TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 
       14.14        13.45         4.80        10.09        12.26        43.00 
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        33.30        34.26 
TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15O 
       32.02        27.12        23.34        20.71        12.92        13.02 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1LA TCGA-E2-A56Z 
       14.07        14.99        38.30        32.78        24.59         8.28 
TCGA-E2-A9RU TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 
       12.85        36.56        35.24         9.86        11.90        34.95 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 
        2.76        21.21        34.65         6.58        21.27        12.53 
TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A5UO TCGA-E9-A5UP 
       41.03        27.22         0.72        29.72        13.81        14.40 
TCGA-EW-A1IW TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1OZ 
       12.20        16.57        15.68        28.77        29.85        40.41 
TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GM-A2D9 
       23.11        18.90        13.94        52.73        22.09        59.57 
TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A66O TCGA-PE-A5DC 
       15.32         2.63        12.36        22.32        17.36        47.01 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-UL-AAZ6 
        0.16        16.50        13.12        16.93        13.94        17.03 
TCGA-Z7-A8R6 
      107.05 

$subtype2
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SF 
       40.14        11.44        48.56        48.36         8.52        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04W 
       14.27        47.24       104.81        78.41        63.12       101.98 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        99.12       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES 
      107.93        61.58       101.72       134.40       107.61        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 
       61.94        24.72        99.19        54.64        44.28        17.13 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       17.46        18.90        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 
       49.48        19.33        48.46        22.45        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       52.47       107.70        17.19        10.59        20.88        39.65 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       32.75        49.48        50.37        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       26.96        34.29        35.47        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       24.26        23.80        11.34        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A07E TCGA-A8-A07J 
       11.97        10.72        11.05        13.02        19.99        12.00 
TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A09T 
        7.99         0.99       112.08        40.01        41.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
       15.02        14.01         0.99        38.04         2.37        10.85 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
        1.48        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92         2.27        32.45        16.31        22.19        14.99 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VC 
       19.79        23.24        24.79        18.67        12.26         0.03 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FN TCGA-AN-A0FS 
        1.32         2.30         0.33         5.65         7.17         6.28 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J8 
        0.33         0.33         5.33        58.95        26.04        22.36 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 
       21.53        50.86        21.37        62.04        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12H TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 
      106.78        98.27        28.37        14.73        32.52        19.20 
TCGA-AR-A0TS TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       74.79        64.83        52.77        48.82        76.11        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       43.56        43.07        37.81        76.21        63.62        62.14 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       96.89        78.51        84.20         2.76        76.01        50.96 
TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM 
       83.77        73.18       143.21        20.25        62.86        52.11 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        16.04        20.45        10.59 
TCGA-B6-A0I5 TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RI 
      149.59        50.70       126.12        84.59       110.93       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
       78.02       172.96       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      188.68       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       73.51        85.35        71.15        28.50        46.95        40.83 
TCGA-BH-A0B7 TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BZ 
       56.98        61.68        35.67        27.19        53.95        49.05 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO 
       48.13        31.17        23.44        38.01        13.91        17.26 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA 
       38.47        67.86        47.41        15.68        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA 
       24.49        31.00        37.78        35.51        24.56        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0RX TCGA-BH-A0W4 
       20.38         5.85         2.50        13.61         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A1ET 
       42.35        44.81         2.01        20.12        72.56        82.85 
TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FE 
       42.28        49.58        25.81        89.16       120.62        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU 
      122.89        36.92        63.35        55.00       144.59        72.07 
TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ 
       10.65        20.12       109.28         8.94         5.26        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A1HE TCGA-C8-A1HI 
       21.76         9.44        11.77        12.66        12.33        11.28 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A8HP 
        0.30         0.36         0.43         0.03         0.03        13.02 
TCGA-C8-A8HR TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH 
       13.41        20.58        13.48        21.14        18.71        14.01 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB 
       20.38        12.20        14.70        16.73        25.74        18.15 
TCGA-D8-A1XC TCGA-D8-A1XM TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27I TCGA-D8-A27K 
       12.39        17.69        15.16        17.42        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       16.41         0.76        13.08        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10F TCGA-E2-A14N 
       16.18         8.02        27.52        40.41        28.87        47.15 
TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C 
       38.24        43.33        28.60        21.04        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P 
       17.29        17.42        19.40         9.04        20.58        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IF 
       53.03        33.01        32.35        28.50        16.47        37.41 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       28.44        22.65         3.88        11.08        54.18        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N3 TCGA-E9-A1N4 
       40.47        28.90        15.72        30.61        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA 
       36.82        35.77        25.84        28.27         6.12        32.09 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H 
        1.12        35.64        32.05        13.32        39.09        20.71 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
       17.06         1.94        24.56         0.76        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       12.33        14.70        39.72         8.48        18.21        13.25 
TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PE 
       29.95        39.78        52.96        18.48        30.08        10.52 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A2DA TCGA-GM-A2DB 
       34.55        55.00        34.03        23.51       216.76        79.10 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62        85.35        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        62.43        11.84        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO 
       10.62        24.95        10.95        25.05        17.06        14.47 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        7.46        14.50        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       58.62        40.08        34.92        28.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY 
       65.62        42.77        14.07        19.73        40.11         0.26 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 
       13.84        15.35        14.96        13.84        11.41        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

$subtype3
TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A3XU 
       43.43        20.88        75.55        98.99        56.81        29.98 
TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07Z 
       21.14        33.11        14.70        26.01        18.97        45.07 
TCGA-A8-A084 TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A0A1 
       15.06        28.96        17.95         9.99        12.00        12.00 
TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A3OD TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6NO 
       19.04        17.03        14.83         1.55        17.42         1.68 
TCGA-AN-A0FK TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03N TCGA-AO-A0J7 TCGA-AO-A0J9 
        7.00        12.33         0.30        66.77        20.32        53.03 
TCGA-AO-A12A TCGA-AR-A0TR TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A5QM TCGA-B6-A0IB 
       90.58         5.26        61.28        50.89        54.74       129.57 
TCGA-B6-A0IH TCGA-B6-A0RH TCGA-B6-A0RP TCGA-B6-A0WW TCGA-B6-A40B TCGA-BH-A0B5 
      112.37       189.01       102.77        18.35       103.63        48.36 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0E9 
       37.22        21.70        49.94        44.02        15.65        46.19 
TCGA-BH-A0GZ TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18P 
       10.78        36.85        12.89         8.81        90.84        30.28 
TCGA-BH-A1EV TCGA-BH-A202 TCGA-BH-A28Q TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A274 
       12.00        26.14         6.44         9.63         9.70         9.53 
TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A27V 
       14.17        16.50        14.73        15.55        15.85        12.53 
TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 TCGA-E2-A154 
       12.10        34.42        37.51        28.44        23.24        19.43 
TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A2P6 TCGA-E9-A1R3 
       18.21        17.10        33.73        39.62         5.52         2.56 
TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A6HE TCGA-EW-A1PC 
        3.02        40.24         7.13        26.07        15.39         6.15 
TCGA-EW-A423 TCGA-GM-A3NW TCGA-LD-A66U TCGA-LL-A6FP TCGA-LQ-A4E4 TCGA-OL-A66K 
       10.16       110.50        21.24        22.26        27.91        41.92 
TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-AA0Z TCGA-WT-AB44 
       26.04         8.91        64.21        86.96        16.80        29.03 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       31.79        28.01        19.20        18.02        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ 
       24.79       107.93        67.33        34.55        33.76        79.76 
TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ 
       63.29        50.43        17.52         8.38        18.21        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        83.01        47.31        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.37         7.30        21.90        35.31        37.45        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE 
       31.73        20.19        23.74        21.73        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.29         9.37        10.42         8.75 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B 
       31.00        17.03         9.99         8.98        24.99        38.01 
TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09D TCGA-A8-A09N 
        9.99         0.99        43.00        30.97        50.04         1.02 
TCGA-A8-A09Q TCGA-AC-A23C TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X 
       25.02         0.95        38.53        33.04        16.57        13.71 
TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.12         1.78         1.71         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         0.33         6.44         7.96         7.59 
TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XT 
        7.04         0.33         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        29.13        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       102.58       108.03        64.04        48.36        41.62 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TT 
       70.39        26.93       130.09         2.56       111.32        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 
       42.35        98.93        55.86        65.36       101.95        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q 
       75.55        61.84        17.23        33.73       160.90       104.28 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 
       97.84        53.36        78.48        93.83        20.38        77.62 
TCGA-B6-A0I2 TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IQ 
      143.38        65.72       176.98        18.77       110.14       140.88 
TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      211.56       100.70       131.21        21.47       186.48       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B9 
       74.99        59.84        20.45        39.55        56.94        51.68 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BW 
       25.71        24.85        44.05        48.69        53.69        11.67 
TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0GY TCGA-BH-A0H9 TCGA-BH-A0WA 
       41.75         4.41         9.63        30.35        41.00        23.05 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FN 
       55.63         7.36        51.16        17.69        97.48        72.07 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P 
       38.60        57.83       130.16        18.64        11.93        11.77 
TCGA-C8-A12U TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HF 
       12.66         3.16         2.24         1.12         1.05        10.92 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z 
        0.16         2.30         0.23         9.50         0.99        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ 
       13.97        14.17        19.20        12.03        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ 
       20.12        20.09        19.40        21.01        18.58        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ 
       14.50        19.92        16.41        12.99        12.66        15.32 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z 
       16.04        13.05        13.48        38.60        31.96        18.51 
TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II 
       25.41        14.79        25.05        11.05        60.53        33.70 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 
       20.98        27.42       106.75       102.61        43.04        16.93 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND 
       34.92        26.56        12.00        13.12        39.55        12.59 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 
       34.59        34.13        22.75        12.89        23.51         0.69 
TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 
       30.18         0.79        18.90        25.94        22.82        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A3U0 
        7.86        19.99        14.43        19.96        25.91        17.49 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A7W5 
        7.40       109.87        70.85        69.30         2.60         7.10 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 
       11.44        14.70        14.79        16.08        15.68        14.73 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ 
       58.52        36.36        20.38        23.47        28.21         9.93 
TCGA-S3-AA10 TCGA-UU-A93S 
       15.39         3.81 

$subtype5
TCGA-A2-A0CU TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25D TCGA-A8-A082 TCGA-A8-A091 
        5.19        23.47        20.25        18.15        18.05        33.01 
TCGA-AC-A6IW TCGA-AO-A03R TCGA-AO-A1KP TCGA-B6-A0IA TCGA-B6-A1KC TCGA-B6-A2IU 
       13.58        68.75        82.62       220.90        43.59       170.17 
TCGA-BH-A0AY TCGA-BH-A0BT TCGA-BH-A0DS TCGA-BH-A0H0 TCGA-BH-A0HB TCGA-BH-A1EO 
       25.55        45.57         2.56        15.16        26.50        91.99 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A204 TCGA-C8-A12X TCGA-D8-A1X6 TCGA-D8-A1XD 
      114.15        33.17        83.31        12.66        17.79        17.16 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-E2-A10C TCGA-E2-A15F TCGA-E2-A15R TCGA-E2-A1B0 
        9.93        14.24        40.11        21.63        17.06        53.62 
TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1RB 
       22.19        18.87         8.75        34.29        13.48        32.09 
TCGA-E9-A54Y TCGA-EW-A1P0 TCGA-GM-A2DC TCGA-JL-A3YX TCGA-LL-A7SZ TCGA-LL-A9Q3 
       23.84        41.13        83.34        11.57        14.70        14.07 
TCGA-WT-AB41 
       52.96 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.16     0.03     0.30     0.16     2.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
  162.05   234.28   189.01   211.56   220.90 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.110   28.405   21.010   22.325   23.470 
[1] "0.2 - 162.1 (23.1)" "0.0 - 234.3 (28.4)" "0.3 - 189.0 (21.0)"
[4] "0.2 - 211.6 (22.3)" "2.6 - 220.9 (23.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      13       17        2        0        88        64         1
  subtype2      48       42        5        2       112        86         1
  subtype3       6        4        0        1        33        28         0
  subtype4      19       15        1        0       103        56         0
  subtype5       3        3        0        0        17        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         48         13         14        8         0       3
  subtype2         56          6         28        6         0       7
  subtype3          9          4          7        2         0       2
  subtype4         31          6         11        4         1       1
  subtype5          6          0          3        0         0       0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          13       48        6       19        3
  STAGE IA         17       42        4       15        3
  STAGE IB          2        5        0        1        0
  STAGE II          0        2        1        0        0
  STAGE IIA        88      112       33      103       17
  STAGE IIB        64       86       28       56       11
  STAGE III         1        1        0        0        0
  STAGE IIIA       48       56        9       31        6
  STAGE IIIB       13        6        4        6        0
  STAGE IIIC       14       28        7       11        3
  STAGE IV          8        6        2        4        0
  STAGE TIS         0        0        0        1        0
  STAGE X           3        7        2        1        0
[1] 13  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  56 175  25  14
  subtype2 142 183  65   9
  subtype3  13  63  14   7
  subtype4  48 170  22   9
  subtype5  13  25   4   1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       56      142       13       48       13
  T2      175      183       63      170       25
  T3       25       65       14       22        4
  T4       14        9        7        9        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 101 101  42  18
  subtype2 198 129  34  31
  subtype3  44  35   6  10
  subtype4 141  67  30  13
  subtype5  17  18   5   3
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0      101      198       44      141       17
  N1      101      129       35       67       18
  N2       42       34        6       30        5
  N3       18       31       10       13        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus         0   1
  subtype1 233   9
  subtype2 317   6
  subtype3  79   2
  subtype4 216   4
  subtype5  34   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  233    9
  subtype2  317    6
  subtype3   79    2
  subtype4  216    4
  subtype5   34    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      233      317       79      216       34
  1        9        6        2        4        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1 261  10
  subtype2 400   0
  subtype3  96   1
  subtype4 251   0
  subtype5  43   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  261   10
  subtype2  400    0
  subtype3   96    1
  subtype4  251    0
  subtype5   43    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      261      400       96      251       43
  MALE         10        0        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           228
  subtype2                          0                           230
  subtype3                          0                            53
  subtype4                          1                           223
  subtype5                          0                            29
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             24                   0
  subtype2                            119                   0
  subtype3                             36                   0
  subtype4                              5                   5
  subtype5                              8                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                6
  subtype2                     3                               14
  subtype3                     0                                5
  subtype4                     1                                4
  subtype5                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  4              9
  subtype2                 12             22
  subtype3                  0              3
  subtype4                  0             11
  subtype5                  1              3
D3V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA         228      230       53      223       29
  INFILTRATING LOBULAR CARCINOMA         24      119       36        5        8
  MEDULLARY CARCINOMA                     0        0        0        5        1
  METAPLASTIC CARCINOMA                   0        3        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        6       14        5        4        1
  MUCINOUS CARCINOMA                      4       12        0        0        1
  OTHER  SPECIFY                          9       22        3       11        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"
D3V9, binary
          cls
clus         0   1
  subtype1  78 193
  subtype2  93 307
  subtype3  26  71
  subtype4  77 174
  subtype5  14  29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78  193
  subtype2   93  307
  subtype3   26   71
  subtype4   77  174
  subtype5   14   29
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        78       93       26       77       14
  YES      193      307       71      174       29
[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"
D3V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    22                        39
  subtype2                                1    18                        51
  subtype3                                0     3                         9
  subtype4                                0    15                        64
  subtype5                                0     2                         7
          vv
clus       WHITE
  subtype1   170
  subtype2   306
  subtype3    73
  subtype4   155
  subtype5    32
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                  22       18        3       15        2
  BLACK OR AFRICAN AMERICAN              39       51        9       64        7
  WHITE                                 170      306       73      155       32
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
          cls
clus         0   1
  subtype1   9 210
  subtype2  17 332
  subtype3   3  72
  subtype4   8 208
  subtype5   1  36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  210
  subtype2   17  332
  subtype3    3   72
  subtype4    8  208
  subtype5    1   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            9       17        3        8        1
  NOT HISPANIC OR LATINO      210      332       72      208       36
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 134  18
  subtype2  94  17
  subtype3 160  15
  subtype4 117  11
  subtype5 106  20
  subtype6  49   5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     152      111      175      128      126       54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       17       15       11       20        5 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SQ 
      129.14       131.67        42.81        14.27        13.68        18.21 
TCGA-A2-A04R TCGA-A2-A0CT TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
      121.94        75.25        20.75        21.90        21.67        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25E 
       23.47        17.36        60.72        19.56        42.44       105.34 
TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A26E TCGA-A7-A26J TCGA-A7-A2KD TCGA-A8-A075 
       21.90        37.45        31.36        20.61        22.32        17.03 
TCGA-A8-A08O TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V TCGA-AN-A0XT 
       31.00         5.72        99.35        26.04        11.44         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A0JI 
       80.28        61.35        21.53        72.00        26.24        50.24 
TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0TW 
       65.56        82.62        61.87         0.53        73.64        98.93 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A24L TCGA-AR-A24S TCGA-AR-A24V 
      107.24        83.87       114.02        94.22        97.84        85.35 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-B6-A0RG TCGA-B6-A0RO TCGA-B6-A0WT TCGA-B6-A0WV 
       79.00        89.00        68.45       162.05       188.68        79.63 
TCGA-B6-A0WY TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU 
      113.79        68.94        43.59       139.17        68.12        24.53 
TCGA-BH-A0AW TCGA-BH-A0B8 TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0DQ TCGA-BH-A0E2 
       20.45        51.58        45.57        49.05         3.22        14.30 
TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HX 
       30.35        15.16        23.08        52.96        26.50        27.25 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FM 
       91.99       113.82        31.53        89.16        24.66        45.63 
TCGA-BH-A204 TCGA-BH-A6R8 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       83.31         9.63        11.34        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A8HQ 
        3.25         0.43         8.28         9.67        12.20        12.49 
TCGA-C8-A9FZ TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XD 
       19.46        16.50        15.78        18.58        23.90        17.16 
TCGA-D8-A1XF TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27R TCGA-D8-A27W 
       15.22        16.54        15.32        15.52        10.09        12.26 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A15K TCGA-E2-A1IE 
       43.00        59.41        46.59        40.11         9.04        38.30 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1LA TCGA-E2-A56Z 
       32.78        33.73        22.19        20.98        24.59         8.28 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE 
       13.48        13.12         9.86         2.76        21.21        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A295 TCGA-E9-A5UO 
        6.58        21.27        12.53        22.75         0.72        13.81 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P6 TCGA-EW-A1PA 
       18.90        28.77        29.95        29.85        18.48        18.90 
TCGA-EW-A1PF TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GM-A2DA TCGA-GM-A2DC 
       14.43        52.73        25.91        22.09       216.76        83.34 
TCGA-GM-A2DK TCGA-JL-A3YX TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-OL-A5RZ 
       86.96        11.57        22.26        12.36        14.07        22.32 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA11 
       26.70        65.62        17.36        16.50        16.93        13.84 
TCGA-S3-AA12 TCGA-UL-AAZ6 
       15.35        17.03 

$subtype2
TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0SV TCGA-A2-A0SW 
       40.14         9.96        48.10        39.32        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3XV 
       44.28        20.52        18.90        18.15        20.88        32.75 
TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A4SC TCGA-A7-A4SF TCGA-AC-A23C TCGA-AC-A2B8 
       25.15        23.80        14.66        17.92         0.95         1.48 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XV 
        8.22        20.19         2.30         0.33        12.33         5.33 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KT TCGA-AQ-A04H 
       76.77        71.80        57.30        41.62        17.79        24.79 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AR-A0TV TCGA-AR-A1AP TCGA-AR-A1AT 
      130.09         5.65        15.62        42.35        39.98        41.82 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A255 TCGA-AR-A2LK 
       61.28       160.90        78.51        87.22        58.92        54.21 
TCGA-AR-A2LL TCGA-AR-A5QN TCGA-B6-A0RL TCGA-B6-A0WW TCGA-B6-A40B TCGA-B6-A40C 
       66.15        16.04        81.17        18.35       103.63        71.15 
TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DS TCGA-BH-A0HK TCGA-BH-A0HY 
       45.83        38.01        13.91         2.56         5.85        50.79 
TCGA-BH-A1EN TCGA-BH-A1EY TCGA-BH-A1FD TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A42T 
       69.93        17.69        33.17        26.14        38.60        10.52 
TCGA-BH-AB28 TCGA-C8-A26V TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M8 TCGA-D8-A1J8 
        9.44         0.30         9.53         0.03         0.23        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1XA TCGA-D8-A1XJ 
       17.49        12.03        20.09        20.38        27.58        21.83 
TCGA-D8-A1XU TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N TCGA-E2-A1BD 
       12.99         9.93        14.14        13.45         4.80        17.10 
TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1NA 
       28.90        16.93         5.52        34.29        12.85        36.56 
TCGA-E9-A1NF TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A54Y 
       35.24         3.02        40.24        27.22        29.72        23.84 
TCGA-EW-A1IW TCGA-EW-A1J5 TCGA-EW-A1OZ TCGA-EW-A1PC TCGA-EW-A3E8 TCGA-EW-A423 
       12.20        15.68        40.41         6.15        34.03        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2DL TCGA-GM-A3NW TCGA-GM-A3NY TCGA-LL-A5YL 
       23.51         7.40       115.69       110.50        38.20        17.06 
TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-OL-A66K TCGA-OL-A66L 
       15.32         2.63        14.50        27.91        41.92        42.77 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-S3-AA17 
       26.04        13.12        13.94 

$subtype3
TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A2-A0CO 
       11.44        48.56        43.43        47.24        20.88       114.81 
TCGA-A2-A0EU TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YL 
       34.29        17.46        32.55        25.28        50.47        48.46 
TCGA-A2-A1G0 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A3KD TCGA-A2-A4S2 TCGA-A7-A13H 
       20.25       107.70        17.19        39.65        21.14        29.56 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SB TCGA-A7-A6VX TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2FG TCGA-AC-A2QI 
       13.74        10.42        38.04         2.37        36.99         0.92 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AC-A6NO 
       16.31        22.19        14.99        24.79        17.42         1.68 
TCGA-AC-A8OR TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AO-A03N 
        1.32         0.33         0.30         0.33         0.33        66.77 
TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AQ-A1H3 
       21.37        62.04        99.25       108.72        98.27        32.52 
TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS 
        5.26        51.25        48.82        76.11        43.73        37.81 
TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24P TCGA-AR-A24X TCGA-AR-A2LE TCGA-AR-A2LM 
       50.89        96.89         2.76        83.77       143.21        52.11 
TCGA-AR-A2LN TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0WZ 
       38.17       234.28        78.02       172.96       102.77       129.57 
TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A2IU TCGA-BH-A0AZ TCGA-BH-A0B5 
       28.27        58.88        73.51       170.17        28.50        48.36 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BS TCGA-BH-A0DP 
       37.22        32.02        21.70        61.68        53.95        15.65 
TCGA-BH-A0E1 TCGA-BH-A0H6 TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0HP 
       15.68        24.56        23.90        20.38        16.96        13.61 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1FJ TCGA-BH-A1FL 
       23.93        24.95        82.85        49.58        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A28Q TCGA-BH-A8FY TCGA-C8-A1HE TCGA-D8-A1JD TCGA-D8-A1JE 
      144.59         6.44         9.70        12.33        18.15        18.90 
TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       18.97        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       25.74        18.15        12.39        15.55        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       15.16        17.42         9.44         0.76        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B 
       33.37        18.51         8.02        12.10        34.42        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A1B4 TCGA-E2-A1BC 
       28.44        28.87        17.42        19.40        33.01        16.47 
TCGA-E2-A1IF TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
       37.41         3.88        11.08        54.18        39.62        19.66 
TCGA-E2-A570 TCGA-E2-A572 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1R0 
       30.61        39.72        34.82        32.88        36.82        28.27 
TCGA-E9-A1R3 TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
        2.56         1.12        35.64        34.13        32.05        13.32 
TCGA-E9-A22H TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X 
       20.71         7.13        24.56        26.07        18.41        12.33 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1P0 
       14.40        15.39        39.72        13.25        16.57        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PE TCGA-GM-A2D9 TCGA-GM-A5PV TCGA-GM-A5PX 
       52.96        23.11        10.52        59.57        13.55        18.12 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-MS-A51U TCGA-OL-A5RV 
       21.24        13.28        10.95        25.05        22.39        34.92 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LX TCGA-S3-AA14 TCGA-W8-A86G TCGA-WT-AB44 
       19.73        40.11         0.16        14.96        11.41        29.03 
TCGA-Z7-A8R6 
      107.05 

$subtype4
TCGA-5L-AAT1 TCGA-A2-A0CR TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ST TCGA-A2-A0T1 
       48.36       107.93       134.40       107.61        99.19        17.13 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A25F TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A7-A3IY 
       49.48        19.33        10.59        49.48        50.37        11.34 
TCGA-A7-A4SA TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO 
       14.93        10.85        40.57        55.43        38.79        50.70 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A6IV 
        2.27        32.45        19.79        23.24         1.55        18.67 
TCGA-AC-A8OQ TCGA-AN-A0XW TCGA-AO-A03U TCGA-AO-A0JC TCGA-AO-A128 TCGA-AQ-A7U7 
        1.12         5.59        58.95        50.86       106.78        19.20 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AW TCGA-AR-A1AX 
       86.66        64.83        52.77        43.56        63.62        62.14 
TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LO TCGA-AR-A2LQ 
       84.20        53.36        73.18        20.25        39.39        40.54 
TCGA-AR-A5QQ TCGA-B6-A0RT TCGA-B6-A401 TCGA-BH-A0B6 TCGA-BH-A0BF TCGA-BH-A0C0 
       10.59        89.46        85.35        56.94        25.71        41.75 
TCGA-BH-A0C3 TCGA-BH-A0DV TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A1EU TCGA-BH-A1F0 
       48.13        67.86         5.59        42.35        42.28        25.81 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FU TCGA-BH-A209 TCGA-BH-A2L8 TCGA-BH-A42U 
      120.62        74.73        72.07       130.16        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A26W TCGA-C8-A26X 
        8.94         5.26        18.87        21.76         0.23         0.36 
TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1Y2 
        9.50         0.03        13.02        13.41        18.71        14.24 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A73U TCGA-E2-A108 TCGA-E2-A1B1 
       14.43        16.41        13.48        16.18        27.52        53.03 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A3DX 
       32.35        28.50        33.70        28.44        22.65        15.72 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A22D 
       35.77        25.84        11.90         6.12        32.09        41.03 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-EW-A1IY 
       17.06         1.94         0.76        30.18        15.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1OV TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PG TCGA-EW-A3U0 
       18.21        25.94        39.78        30.08        34.55        17.49 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A2DO 
       75.02        70.85        72.10        85.15       101.62        85.35 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       66.38        72.03         7.10        10.62        24.95        11.44 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A66I 
       14.70        14.47        14.70        40.08        24.72        23.47 
TCGA-OL-A66P TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA15 TCGA-WT-AB41 TCGA-XX-A899 
       14.07         0.26         9.93        13.84        52.96        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

$subtype5
TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A0SX TCGA-A2-A0T0 
        8.52        31.79        28.01        19.20        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS 
        8.38        18.21        18.61        31.73        19.20        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       83.01        29.98        47.31        34.98        38.37        24.39 
TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       26.96        31.73        20.19        24.26        23.74        21.73 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.50        21.17        12.10        10.29         9.37         8.75 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A7VC 
       38.53        33.04        16.57        13.71        13.58         0.03 
TCGA-AN-A0XU TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A1KO 
        0.33        50.70        55.33       102.58       108.03        14.73 
TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       70.39         2.56       111.32        13.71        65.36        85.97 
TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 
       61.84        43.07        17.23        33.73       104.28        78.48 
TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU 
       93.83        20.38        77.62       211.56       100.70       131.21 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0B3 TCGA-BH-A0B9 
       21.47       186.48       101.52        74.99        39.55        51.68 
TCGA-BH-A0E0 TCGA-BH-A0H9 TCGA-BH-A0WA TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN 
        4.41        41.00        23.05        97.48       114.15        72.07 
TCGA-BH-A208 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL 
       57.83         0.16         0.99        12.03        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A27F 
       19.40        14.50        16.41         6.35        12.66        16.04 
TCGA-D8-A27H TCGA-E2-A14N TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1LG TCGA-E2-A1LH 
       13.05        47.15        60.53        53.62        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 
      102.61         8.75        43.04        15.45        34.92        26.56 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22E 
       12.00        39.55        12.59        32.09        34.59        12.89 
TCGA-E9-A22G TCGA-E9-A244 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB 
       23.51         0.69        22.82        29.82         7.86        19.99 
TCGA-EW-A1PH TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       19.96       109.87        79.10        69.30         2.60        11.84 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5RW 
       14.79        16.08        15.68         7.46        14.73        36.36 
TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-OL-A97C TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UU-A93S 
       20.38        28.21         8.91        16.80        15.39         3.81 

$subtype6
TCGA-A1-A0SM TCGA-A2-A0CK TCGA-A2-A0SU TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 
        7.96       136.73        54.64        22.45        16.47        52.47 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A7-A13G TCGA-A7-A5ZW TCGA-A7-A5ZX 
        7.30        21.30        23.21        23.61        10.72        11.05 
TCGA-A8-A0A6 TCGA-AC-A3OD TCGA-AC-A6IX TCGA-AQ-A54O TCGA-AR-A1AU TCGA-AR-A24T 
       21.04        14.83        12.26        32.91        76.21        76.01 
TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A2LJ TCGA-AR-A5QP TCGA-B6-A0IK TCGA-B6-A0RV 
       50.96        72.76        62.86        20.45        18.77       157.41 
TCGA-BH-A0B2 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A1EV 
       40.83        23.44        22.13        10.78        37.78        12.00 
TCGA-BH-A1EW TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-C8-A1HF 
       55.69       122.89        36.92        28.14        10.65        10.92 
TCGA-C8-A1HI TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM 
       11.28        14.01        21.01        14.73        19.92        17.69 
TCGA-D8-A4Z1 TCGA-E2-A14U TCGA-E2-A1L7 TCGA-E2-A1LB TCGA-E9-A1R2 TCGA-E9-A22A 
       21.67        43.33        27.42        40.47        34.95        39.09 
TCGA-EW-A1PD TCGA-EW-A2FR TCGA-GM-A2DM TCGA-GM-A3XG TCGA-LD-A74U TCGA-OL-A5RX 
       13.94        55.00       106.06        43.73        13.22        28.87 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.33     0.03     0.16     0.03     0.03     7.30 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  216.76   160.90   234.28   134.40   211.56   157.41 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.620   20.880   22.390   26.730   23.280   23.325 
[1] "0.3 - 216.8 (23.6)" "0.0 - 160.9 (20.9)" "0.2 - 234.3 (22.4)"
[4] "0.0 - 134.4 (26.7)" "0.0 - 211.6 (23.3)" "7.3 - 157.4 (23.3)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      10        6        2        0        44        41         0
  subtype2       7       11        0        1        31        25         1
  subtype3      14       19        1        1        49        46         0
  subtype4      19       10        1        0        41        25         1
  subtype5       6        8        0        0        58        33         0
  subtype6       5        6        0        0        14         6         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         30          7          9        2       1
  subtype2         22          2          8        2       1
  subtype3         27          4         13        1       2
  subtype4         20          3          7        1       0
  subtype5         12          1          3        4       1
  subtype6         10          2         10        1       0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          10        7       14       19        6        5
  STAGE IA          6       11       19       10        8        6
  STAGE IB          2        0        1        1        0        0
  STAGE II          0        1        1        0        0        0
  STAGE IIA        44       31       49       41       58       14
  STAGE IIB        41       25       46       25       33        6
  STAGE III         0        1        0        1        0        0
  STAGE IIIA       30       22       27       20       12       10
  STAGE IIIB        7        2        4        3        1        2
  STAGE IIIC        9        8       13        7        3       10
  STAGE IV          2        2        1        1        4        1
  STAGE X           1        1        2        0        1        0
[1] 12  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 31 94 19  8
  subtype2 25 63 20  3
  subtype3 53 95 24  4
  subtype4 50 60 15  3
  subtype5 21 87 14  4
  subtype6 15 28  9  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       31       25       53       50       21       15
  T2       94       63       95       60       87       28
  T3       19       20       24       15       14        9
  T4        8        3        4        3        4        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 50 67 22 10
  subtype2 53 29 18  8
  subtype3 72 71 18 13
  subtype4 62 42 16  8
  subtype5 77 33 11  5
  subtype6 20 16  7 10
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       50       53       72       62       77       20
  N1       67       29       71       42       33       16
  N2       22       18       18       16       11        7
  N3       10        8       13        8        5       10
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1 127   3
  subtype2  77   2
  subtype3 140   1
  subtype4  97   1
  subtype5 104   4
  subtype6  45   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127    3
  subtype2   77    2
  subtype3  140    1
  subtype4   97    1
  subtype5  104    4
  subtype6   45    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      127       77      140       97      104       45
  1        3        2        1        1        4        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1 151   2
  subtype2 109   2
  subtype3 176   1
  subtype4 128   0
  subtype5 127   0
  subtype6  51   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151    2
  subtype2  109    2
  subtype3  176    1
  subtype4  128    0
  subtype5  127    0
  subtype6   51    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      151      109      176      128      127       51
  MALE          2        2        1        0        0        3
[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                           126
  subtype2                          0                            67
  subtype3                          0                            88
  subtype4                          0                            78
  subtype5                          1                           102
  subtype6                          0                            37
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             11                   0
  subtype2                             37                   0
  subtype3                             57                   0
  subtype4                             40                   2
  subtype5                              4                   4
  subtype6                             15                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                                5
  subtype2                     0                                4
  subtype3                     0                               12
  subtype4                     2                                2
  subtype5                     1                                1
  subtype6                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  5              6
  subtype2                  0              3
  subtype3                  8             12
  subtype4                  1              3
  subtype5                  0             13
  subtype6                  1              0
D4V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         126       67       88       78      102
  INFILTRATING LOBULAR CARCINOMA         11       37       57       40        4
  MEDULLARY CARCINOMA                     0        0        0        2        4
  METAPLASTIC CARCINOMA                   0        0        0        2        1
  MIXED HISTOLOGY (PLEASE SPECIFY)        5        4       12        2        1
  MUCINOUS CARCINOMA                      5        0        8        1        0
  OTHER  SPECIFY                          6        3       12        3       13
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          37
  INFILTRATING LOBULAR CARCINOMA         15
  MEDULLARY CARCINOMA                     0
  METAPLASTIC CARCINOMA                   0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      1
  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"
D4V9, binary
          cls
clus         0   1
  subtype1  59  94
  subtype2  28  83
  subtype3  50 127
  subtype4  30  98
  subtype5  42  85
  subtype6  11  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   94
  subtype2   28   83
  subtype3   50  127
  subtype4   30   98
  subtype5   42   85
  subtype6   11   43
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        59       28       50       30       42       11
  YES       94       83      127       98       85       43
[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"
D4V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    14                        26
  subtype2                                0     4                        22
  subtype3                                0     4                        15
  subtype4                                1     9                        26
  subtype5                                0     4                        47
  subtype6                                0     2                         7
          vv
clus       WHITE
  subtype1   110
  subtype2    82
  subtype3   156
  subtype4    89
  subtype5    73
  subtype6    44
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                  14        4        4        9        4
  BLACK OR AFRICAN AMERICAN              26       22       15       26       47
  WHITE                                 110       82      156       89       73
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   2
  BLACK OR AFRICAN AMERICAN               7
  WHITE                                  44
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus         0   1
  subtype1  10 129
  subtype2   7  97
  subtype3   7 151
  subtype4   7 112
  subtype5   4 110
  subtype6   2  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  129
  subtype2    7   97
  subtype3    7  151
  subtype4    7  112
  subtype5    4  110
  subtype6    2   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO           10        7        7        7        4        2
  NOT HISPANIC OR LATINO      129       97      151      112      110       48
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 122  25
  subtype2 121  14
  subtype3 101  15
subtype1 subtype2 subtype3 
     147      135      116 
subtype1 subtype2 subtype3 
      25       14       15 
$subtype1
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       47.24        31.79        28.01        18.02        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0CY 
      101.98        36.13        99.12        24.79        56.81        55.00 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV 
       67.33        34.55        33.76        79.76        63.29        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-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE TCGA-A7-A0CJ 
       21.90        21.67        18.61        31.73        35.31        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       35.67        31.73        20.19        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07W 
       26.01        17.03        14.01         9.99         8.98         9.99 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09I 
       37.05         9.99        31.00        43.00         9.99        45.07 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04D TCGA-AN-A0AK 
       33.07         8.98        14.01         0.99         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        6.51         0.16         0.33         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L 
        7.59         0.33         0.53         0.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JB 
       61.35        81.63        58.95        32.78        37.48        50.70 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D 
       72.00        76.77        55.33       102.58       108.03        64.04 
TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TU 
       48.36       111.32        73.64        74.79        86.66        13.71 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       42.35        98.93        55.86        65.36       101.95       114.02 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AT TCGA-AR-A1AY 
       75.55        61.84        43.56        43.07        41.82        33.73 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RU TCGA-B6-A0X1 
       32.78        12.13       176.98       140.88       131.21       186.48 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BW TCGA-BH-A0BZ 
       40.83        39.55        51.68        25.71        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0EE 
       41.75        48.13        48.23         4.41        14.30        31.00 
TCGA-BH-A18G TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V 
        2.01        30.28        55.63        37.55         7.36        51.16 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.93        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66         0.39         3.16         1.87         1.12         4.11 
TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        4.08        11.90        20.88        13.97        14.17        19.20 
TCGA-E2-A14P TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       40.96        31.96        28.60        18.51        25.41        27.12 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       14.79        25.05        60.53 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68        63.12        88.60        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EV 
       98.99       107.93        61.58        25.22        80.28        31.82 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YI TCGA-A7-A0CD TCGA-A7-A0CH 
       54.64        17.46        25.28        49.48        38.30        35.47 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A8-A06Z TCGA-A8-A07S TCGA-A8-A07Z 
       33.11        29.79        25.15         1.02         7.99        45.07 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08T 
       18.05        36.95        13.02         0.99        19.96       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E 
       40.01        33.01         9.99        12.00         1.02        49.05 
TCGA-A8-A09W TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FD 
        0.99         0.23         0.62         2.96         9.96         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        5.65         7.00         7.04         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03N TCGA-AO-A03P 
       12.33         0.30         0.33         0.33        66.77        95.70 
TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0JC TCGA-AO-A0JG TCGA-AO-A126 TCGA-AO-A12A 
       21.40        20.32        50.86        26.24       108.72        90.58 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AK 
       98.27        65.56        41.62        28.37         5.26        51.25 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RL 
       37.81        61.28       129.57       146.50       110.14        81.17 
TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-BH-A0B1 TCGA-BH-A0BJ TCGA-BH-A0BM 
       78.02       102.77       129.70        37.74        21.70        61.68 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH 
       27.19        53.95        49.94        42.90        45.83        38.01 
TCGA-BH-A0DK TCGA-BH-A0DT TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0H5 TCGA-BH-A0H9 
       13.91        38.47        44.81        24.49        35.51        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-A18S TCGA-C8-A12M 
       24.95        42.35         8.81        37.74        66.05        11.77 
TCGA-C8-A12X TCGA-D8-A140 TCGA-D8-A145 TCGA-D8-A146 TCGA-E2-A107 TCGA-E2-A109 
       12.66        13.25        13.48        21.14        34.42        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S 
       40.41        37.51        28.44        44.68        38.24        33.17 
TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       32.02        23.24        19.43        21.04        23.87        23.34 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       17.29        20.71        18.21        12.92        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD 
       33.01        16.47        17.10 

$subtype3
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER TCGA-A2-A0ES 
      104.81        78.41        92.48        53.13        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0T3 TCGA-A2-A0T4 
       34.29        61.94        24.72        99.19        49.84        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YK TCGA-A2-A0YL 
       18.90        20.75        32.55        50.47        19.33        48.46 
TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A8-A06P TCGA-A8-A076 TCGA-A8-A079 
       23.77        34.29        37.45        13.02        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A084 TCGA-A8-A08O TCGA-A8-A095 
       19.99        18.97        10.98        15.06        31.00        41.98 
TCGA-A8-A09K TCGA-A8-A0A4 TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A0J5 
       29.98        13.02         6.28         0.33         0.33        26.04 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       22.36        53.03        21.37        50.24        62.04        71.80 
TCGA-AO-A128 TCGA-AO-A12E TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
      106.78        57.30       130.09        64.83       107.24        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A1AW 
       85.97        52.77        48.82        39.98        76.21        63.62 
TCGA-AR-A1AX TCGA-B6-A0I2 TCGA-B6-A0I8 TCGA-B6-A0IK TCGA-B6-A0RG TCGA-B6-A0RH 
       62.14       143.38        24.62        18.77        68.45       189.01 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WX 
      172.96       162.05       140.48        89.46       157.41        21.47 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
       24.53        59.84        25.55        28.50        46.95        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BO TCGA-BH-A0BP 
       48.36        56.98        37.22        32.02        35.67        48.69 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP 
       53.69        45.57        44.02        23.44        22.13        15.65 
TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
        2.56        67.86        15.68         9.63        46.19        32.58 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HN TCGA-BH-A0HP 
       24.43        30.35        24.56        23.08        16.96        13.61 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18U 
       50.79         5.59        20.12        26.66        72.56        51.39 
TCGA-C8-A12N TCGA-C8-A131 TCGA-C8-A135 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14T 
       11.77         2.24         1.05        27.52        40.11        33.30 
TCGA-E2-A14V TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B1 
       34.26        22.82        21.63        11.05        53.62        53.03 
TCGA-E2-A1B5 TCGA-E2-A1B6 
       32.35        28.50 

subtype1 subtype2 subtype3 
    0.16     0.23     0.33 
subtype1 subtype2 subtype3 
  186.48   146.50   189.01 
subtype1 subtype2 subtype3 
   31.00    27.19    34.98 
[1] "0.2 - 186.5 (31.0)" "0.2 - 146.5 (27.2)" "0.3 - 189.0 (35.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       9        6        0        55        36         24          2
  subtype2      13       12        1        45        39         14          6
  subtype3      14        9        3        36        20         24          5
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1         10        8       1
  subtype2          1        3       3
  subtype3          4        3       2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9       13       14
  STAGE IA          6       12        9
  STAGE IB          0        1        3
  STAGE IIA        55       45       36
  STAGE IIB        36       39       20
  STAGE IIIA       24       14       24
  STAGE IIIB        2        6        5
  STAGE IIIC       10        1        4
  STAGE IV          8        3        3
  STAGE X           1        3        2
[1] 10  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  21 106  22   4
  subtype2  36  83  11   6
  subtype3  38  57  17   8
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       21       36       38
  T2      106       83       57
  T3       22       11       17
  T4        4        6        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 71 45 22 12
  subtype2 66 53 10  6
  subtype3 57 34 20  7
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       71       66       57
  N1       45       53       34
  N2       22       10       20
  N3       12        6        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"
D5V6, binary
          cls
clus         0   1
  subtype1 144   8
  subtype2 130   3
  subtype3 113   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  144    8
  subtype2  130    3
  subtype3  113    4
   clus
vv  subtype1 subtype2 subtype3
  0      144      130      113
  1        8        3        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1 153   0
  subtype2 133   4
  subtype3 119   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  153    0
  subtype2  133    4
  subtype3  119    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      153      133      119
  MALE          0        4        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"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                           140                              4
  subtype2                           121                              5
  subtype3                            94                             21
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   1                                1
  subtype2                   0                                4
  subtype3                   0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              7
  subtype2                  2              5
  subtype3                  0              2
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING DUCTAL CARCINOMA         140      121       94
  INFILTRATING LOBULAR CARCINOMA          4        5       21
  MEDULLARY CARCINOMA                     1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        4        3
  MUCINOUS CARCINOMA                      0        2        0
  OTHER  SPECIFY                          7        5        2
[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"
D5V9, binary
          cls
clus        0  1
  subtype1 57 96
  subtype2 45 92
  subtype3 43 77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   96
  subtype2   45   92
  subtype3   43   77
     clus
vv    subtype1 subtype2 subtype3
  NO        57       45       43
  YES       96       92       77
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    16                        14
  subtype2                                0     7                         9
  subtype3                                0     4                         6
          vv
clus       WHITE
  subtype1    97
  subtype2   103
  subtype3    95
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  16        7        4
  BLACK OR AFRICAN AMERICAN              14        9        6
  WHITE                                  97      103       95
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
          cls
clus         0   1
  subtype1   2 113
  subtype2   2 100
  subtype3   2  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  113
  subtype2    2  100
  subtype3    2   85
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        2
  NOT HISPANIC OR LATINO      113      100       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 53  9
  subtype2 43  5
  subtype3 78 13
  subtype4 47  7
  subtype5 97 15
  subtype6 26  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      62       48       91       54      112       31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9        5       13        7       15        5 
$subtype1
TCGA-A1-A0SH TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EO 
       47.24        88.60        75.55        98.99        61.58        80.28 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
       54.64        17.46        25.28        38.30        35.47        30.61 
TCGA-A7-A0DB TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08T 
       33.11         7.99        45.07        13.02         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-AN-A0FF 
       40.01         9.99        12.00         1.02        49.05         5.65 
TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS 
        7.00         0.36         0.33        12.33         0.30         0.33 
TCGA-AO-A12A TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-B6-A0RL TCGA-B6-A0RM 
       90.58         5.26        37.81        61.28        81.17        78.02 
TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-BH-A0B2 TCGA-BH-A0DH TCGA-BH-A0DT TCGA-BH-A0E7 
      102.77       129.70        40.83        38.01        38.47        44.81 
TCGA-BH-A0EB TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18N TCGA-D8-A146 TCGA-E2-A10A 
       24.49        24.95        42.35        37.74        21.14        40.41 
TCGA-E2-A10B TCGA-E2-A14Q TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       37.51        38.24        18.51        23.24        19.43        23.87 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15J TCGA-E2-A15O 
       17.29        20.71        21.63        18.21        19.40        13.02 
TCGA-E2-A1B4 TCGA-E2-A1BD 
       33.01        17.10 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0T4 TCGA-A2-A0T6 
       13.68        34.29        31.82        61.94        20.52        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A8-A07P 
       20.75        49.48        48.46        23.77        34.29        10.98 
TCGA-AN-A049 TCGA-AN-A0XN TCGA-AO-A0J8 TCGA-AO-A0JF TCGA-AO-A12C TCGA-AR-A1AK 
        0.62         0.33        22.36        21.37        65.56        51.25 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-BH-A0AU 
       76.21        63.62       110.14       162.05       140.48        24.53 
TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BO TCGA-BH-A0BP 
       25.55        37.74        32.02        21.70        35.67        48.69 
TCGA-BH-A0BR TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0H6 
       53.69         2.56        46.19        32.58        30.35        24.56 
TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A18F TCGA-BH-A18M TCGA-C8-A12N TCGA-D8-A145 
       16.96        13.61         8.81        72.56        11.77        13.48 
TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A15C TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1BC 
       44.68        33.30        22.82        19.56        53.03        16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL 
       31.79        28.01        18.02        73.84        87.25        99.12 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ST 
       24.79        67.33        34.55        33.76        79.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A075 TCGA-A8-A076 
       35.31        35.67        31.73        20.19        17.03        53.98 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A08L TCGA-A8-A08P TCGA-AN-A04D TCGA-AN-A0AL 
        9.99         8.98         9.99        31.00         1.71         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 
        0.33         0.33         7.96         7.59         0.33         0.53 
TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 
        0.33        58.95        32.78        37.48        55.33       102.58 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
      106.78       108.03        48.36       111.32        74.79        13.71 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-B6-A0I6 TCGA-B6-A0IJ 
       52.77        43.56        43.07        33.73        32.78       176.98 
TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      140.88       189.01        89.46       131.21        21.47       186.48 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 
       59.84        39.55        51.68        11.67        48.23         4.41 
TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-C8-A12P TCGA-C8-A12U 
        2.01        55.63         7.36        51.16        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
       12.66         2.24         1.12        20.88        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       19.20        31.96        25.41        14.79        25.05        60.53 
TCGA-E2-A1B6 
       28.50 

$subtype4
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER TCGA-A2-A0ES 
      104.81        78.41        92.48        53.13        74.40        72.00 
TCGA-A2-A0EX TCGA-A2-A0T3 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YK TCGA-A7-A0D9 
       24.72        49.84        32.55        50.47        19.33        37.45 
TCGA-A8-A06P TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A084 TCGA-A8-A08O TCGA-A8-A095 
       13.02        19.99        18.97        15.06        31.00        41.98 
TCGA-AN-A041 TCGA-AO-A0J5 TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AR-A0TZ TCGA-AR-A1AL 
        0.23        26.04        71.80       130.09       107.24        48.82 
TCGA-AR-A1AX TCGA-B6-A0I2 TCGA-B6-A0I8 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RN 
       62.14       143.38        24.62       146.50        18.77       172.96 
TCGA-B6-A0RV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BM 
      157.41        28.50        46.95        48.36        37.22        61.68 
TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DV 
       45.57        44.02        23.44        22.13        15.65        67.86 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0RX 
       15.68         9.63        24.43        23.08        50.79         5.59 
TCGA-BH-A18J TCGA-BH-A18U TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A1B0 TCGA-E2-A1B5 
       20.12        51.39        27.52        40.11        53.62        32.35 

$subtype5
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CY 
       63.12        36.13        75.25         5.19       107.93        55.00 
TCGA-A2-A0D4 TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YH TCGA-A7-A0DC TCGA-A7-A13F 
       25.22        27.12        44.88        21.67        29.79        25.15 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 
       17.98        29.03        31.00        26.01         1.02         9.01 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09A 
        9.99        18.05        36.95        19.96        33.01         9.99 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A4 
       29.98        33.07         8.98         0.99        14.01        13.02 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD 
        2.96         9.96         7.36         0.16         0.33         6.44 
TCGA-AN-A0FS TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        6.28         0.33         0.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 
       66.77        81.63        95.70        21.40        20.32        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.70        50.86        72.00        26.24        50.24        62.04 
TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TT 
      108.72        98.27        57.30        41.62        28.37        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-B6-A0IB 
       42.35        98.93        55.86       114.02        39.98       129.57 
TCGA-B6-A0RG TCGA-BH-A0B4 TCGA-BH-A0BF TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV 
       68.45        39.16        25.71        27.19        53.95        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DK 
       49.05        41.75        48.13        42.90        45.83        13.91 
TCGA-BH-A0E2 TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL 
       14.30        35.51        41.00        52.96         5.85         2.37 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18S 
       12.89        51.32        27.25        26.66        30.28        66.05 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A138 
       11.77        12.66        12.66        12.66         3.16         4.08 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10E TCGA-E2-A14S 
       11.90        13.25        34.42        46.59        28.44        33.17 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15K TCGA-E2-A15L 
       34.26        32.02        21.04        23.34         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        17.06        14.07        14.99 

$subtype6
TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A07I 
      101.98        56.81        63.29        17.13        21.90        14.01 
TCGA-A8-A08J TCGA-A8-A08X TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AN-A0FT TCGA-AN-A0FV 
       37.05        43.00        45.07         0.99         7.04         0.33 
TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A1AT TCGA-B6-A0I9 
       76.77        64.04        73.64        64.83        41.82        12.13 
TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A18R TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12Z 
       56.98        31.00        37.55        11.93        12.66         0.39 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-E2-A14P TCGA-E2-A14Y TCGA-E2-A152 
        1.87         1.05         4.11        40.96        28.60        27.12 
TCGA-E2-A15H 
       12.92 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.30     0.33     0.33     0.23     0.16     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  129.70   162.05   189.01   172.96   129.57   101.98 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  31.810   31.085   32.780   41.045   28.405   28.600 
[1] "0.3 - 129.7 (31.8)" "0.3 - 162.1 (31.1)" "0.3 - 189.0 (32.8)"
[4] "0.2 - 173.0 (41.0)" "0.2 - 129.6 (28.4)" "0.3 - 102.0 (28.6)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       9        6        1        21        12          5          5
  subtype2       7        5        0        17         8          8          2
  subtype3       5        5        0        43        20         11          1
  subtype4       5        6        2        10        12         12          1
  subtype5       9        5        1        35        33         22          4
  subtype6       1        0        0        10        10          4          0
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1          0        2       3
  subtype2          2        0       0
  subtype3          3        3       0
  subtype4          1        3       2
  subtype5          4        4       1
  subtype6          5        2       0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           9        7        5        5        9        1
  STAGE IA          6        5        5        6        5        0
  STAGE IB          1        0        0        2        1        0
  STAGE IIA        21       17       43       10       35       10
  STAGE IIB        12        8       20       12       33       10
  STAGE IIIA        5        8       11       12       22        4
  STAGE IIIB        5        2        1        1        4        0
  STAGE IIIC        0        2        3        1        4        5
  STAGE IV          2        0        3        3        4        2
  STAGE X           3        0        0        2        1        0
[1] 10  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 22 32  3  6
  subtype2 16 24  7  2
  subtype3 14 68 10  1
  subtype4 18 25  7  4
  subtype5 20 77 18  3
  subtype6  5 20  5  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       22       16       14       18       20        5
  T2       32       24       68       25       77       20
  T3        3        7       10        7       18        5
  T4        6        2        1        4        3        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 35 19  5  3
  subtype2 26 14  6  2
  subtype3 53 25 11  4
  subtype4 21 18 11  3
  subtype5 51 42 16  7
  subtype6  8 14  3  6
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       35       26       53       21       51        8
  N1       19       14       25       18       42       14
  N2        5        6       11       11       16        3
  N3        3        2        4        3        7        6
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1  58   2
  subtype2  49   0
  subtype3  89   3
  subtype4  47   4
  subtype5 114   4
  subtype6  30   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    2
  subtype2   49    0
  subtype3   89    3
  subtype4   47    4
  subtype5  114    4
  subtype6   30    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       58       49       89       47      114       30
  1        2        0        3        4        4        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  63   1
  subtype2  49   0
  subtype3  93   0
  subtype4  54   0
  subtype5 114   4
  subtype6  32   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    1
  subtype2   49    0
  subtype3   93    0
  subtype4   54    0
  subtype5  114    4
  subtype6   32    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       63       49       93       54      114       32
  MALE          1        0        0        0        4        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            59                              1
  subtype2                            39                              9
  subtype3                            86                              0
  subtype4                            43                              8
  subtype5                            99                             10
  subtype6                            29                              2
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                3
  subtype2                   0                                1
  subtype3                   1                                0
  subtype4                   0                                2
  subtype5                   0                                2
  subtype6                   0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              0
  subtype3                  0              6
  subtype4                  0              1
  subtype5                  2              5
  subtype6                  0              1
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          59       39       86       43       99
  INFILTRATING LOBULAR CARCINOMA          1        9        0        8       10
  MEDULLARY CARCINOMA                     0        0        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        1        0        2        2
  MUCINOUS CARCINOMA                      0        0        0        0        2
  OTHER  SPECIFY                          1        0        6        1        5
                                  clus
vv                                 subtype6
  INFILTRATING DUCTAL CARCINOMA          29
  INFILTRATING LOBULAR CARCINOMA          2
  MEDULLARY CARCINOMA                     0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          1
[1] 6 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1 24 40
  subtype2 22 27
  subtype3 41 52
  subtype4 17 37
  subtype5 33 85
  subtype6  8 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   40
  subtype2   22   27
  subtype3   41   52
  subtype4   17   37
  subtype5   33   85
  subtype6    8   24
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        24       22       41       17       33        8
  YES       40       27       52       37       85       24
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         4
  subtype2                                0     1                         1
  subtype3                                0     7                        13
  subtype4                                0     0                         3
  subtype5                                0    10                         7
  subtype6                                1     6                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    44
  subtype3    65
  subtype4    44
  subtype5    79
  subtype6    17
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   3        1        7        0       10
  BLACK OR AFRICAN AMERICAN               4        1       13        3        7
  WHITE                                  46       44       65       44       79
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                   6
  BLACK OR AFRICAN AMERICAN               1
  WHITE                                  17
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
          cls
clus        0  1
  subtype1  1 47
  subtype2  0 36
  subtype3  1 77
  subtype4  2 36
  subtype5  2 78
  subtype6  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   47
  subtype2    0   36
  subtype3    1   77
  subtype4    2   36
  subtype5    2   78
  subtype6    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        1        2        2        0
  NOT HISPANIC OR LATINO       47       36       77       36       78       24
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 475  70
  subtype2 258  43
  subtype3 194  18
subtype1 subtype2 subtype3 
     545      301      212 
subtype1 subtype2 subtype3 
      70       43       18 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14        42.81        40.14        11.44        48.36         9.96 
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       14.27        20.88         7.96        39.32        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT 
      121.94        63.12        36.13        88.60        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER 
        5.19       107.93        61.58        25.22       101.72        74.40 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV 
       35.05        34.29        31.82        63.29        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD 
       44.88        49.84        20.52        17.46        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       50.47        21.67        49.48        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KD 
       60.72        19.56        42.44        17.19       105.34        39.65 
TCGA-A2-A4RW TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
        7.30        23.21        21.14        38.30        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J 
       37.45        25.15        23.61        31.36        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SB 
       22.32        11.34        10.59        10.29        13.41        13.74 
TCGA-A7-A4SF TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T 
       17.92        10.42        13.02        13.02         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       18.97        18.97        14.01        12.00        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99         9.99        45.07        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        28.96        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       37.05        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98        12.00         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       19.04        27.02        17.03        38.04         0.95         2.37 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A3TN TCGA-AC-A3W6 
        1.48        99.35        26.04         0.92        14.99        19.79 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB 
       24.79         1.55        11.44        17.42         1.68         8.22 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        2.96         9.96         7.36         6.44         5.65         7.00 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XP 
        7.04         0.36         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 
       66.77        81.63        95.70        47.87        29.13        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A0JM 
       26.04        20.32        22.36        21.53        50.24        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H 
       99.25       108.72        98.27        65.56        41.62        28.37 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 
       82.62        61.87         0.53        17.79        24.79         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52        32.91        19.20        73.64         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 
       86.66        42.35        98.93        55.86       107.24        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW 
      114.02        43.73        39.98        37.81        61.28        63.62 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P 
      160.90        50.89        94.22        96.89        78.51         2.76 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       87.22        97.84        85.35        83.77        79.00        89.00 
TCGA-AR-A2LE TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0I8 
      143.21        54.21        66.15        54.74       149.59        24.62 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN 
      220.90       129.57        50.70       146.50       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
      110.14        68.45       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      162.05       102.77        97.48       188.68        79.63        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI 
      129.57       129.70        28.27        68.94        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        68.12       103.63        71.15        24.53 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        46.95        37.74        39.16        48.36        56.94 
TCGA-BH-A0B8 TCGA-BH-A0BD TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       51.58        18.21        53.69        53.95        45.57        49.94 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DS 
       44.02        42.90        45.83        38.01         3.22         2.56 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GZ 
       15.68        14.30        44.81        24.49        24.43        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       15.16        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         2.37        16.96         2.50        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I 
       51.32        27.25        50.79        23.93        44.81         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S 
       20.12        90.84        26.66        37.74        30.28        66.05 
TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        91.99       113.82        82.85        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FG 
       17.69        31.53        89.16        24.66        33.17       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A28Q 
       63.35        55.00        45.63       144.59        83.31         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M 
       20.12        10.52        23.51         9.63         9.70        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77        12.66        12.66        12.66        12.66         3.16 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN 
        4.08        12.33        11.34        11.28        10.42         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A 
        0.30         0.23         8.28         9.67         9.53        12.20 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1JC TCGA-D8-A1JD 
        0.23        12.49        13.25        20.58        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.90        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV 
       19.92        15.55        15.85        16.31        12.99        15.16 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.54        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.45        16.41         4.80        10.09        13.08        12.26 
TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A106 
       18.51        16.18         8.02        12.10        43.00        59.41 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       28.87        44.68        33.17        33.30        34.26        32.02 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        9.04        20.58        13.02        17.06        14.07        14.99 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       33.01        16.47        17.10        38.30        32.78        33.73 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.65         3.88        22.19        11.08        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 
       19.66        24.59        16.93         5.52         8.28        30.61 
TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA 
       39.72        34.29        34.82        32.88        36.82        36.56 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       35.24        25.84         9.86        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02         2.76        21.21        32.09        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
        1.12        34.65         6.58        21.27        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        12.53        13.32        39.09        22.75        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       12.89        20.71        27.22         7.13        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO 
       29.72        26.07        18.41        12.33        23.84        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       14.40        15.39        39.72         8.48        18.21        18.90 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        28.77        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA TCGA-EW-A1PD 
       41.13        52.96        23.11        18.48        18.90        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       10.52        14.43        22.09        34.03        10.16        23.51 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
        7.40        59.57        83.34        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
      101.62        85.35        38.20        18.12        11.57        21.24 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
       10.95        25.05        15.32        14.70        22.26         2.63 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 TCGA-OL-A5DA 
       14.70        12.36        14.07        27.91        31.99        58.62 
TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66O TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       26.70        41.92        17.36        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 
       64.21         0.16        16.50        13.12        16.93        13.84 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-WT-AB44 TCGA-Z7-A8R6 
       15.35        13.94        52.96        29.03       107.05 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      131.67         8.52        31.79        28.01        19.20        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CM 
       78.41        73.84        87.25       101.98        55.43        24.79 
TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ 
       56.81        55.00        67.33        34.55        33.76        79.76 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T7 
       99.19        50.43        17.52        17.13         8.38        20.75 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F 
       18.21        21.90        18.61        31.73        19.20        10.59 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        83.01        29.98        32.75        49.48        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 
       34.98        50.37        38.37        24.39        26.96        21.90 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G 
       35.31        35.67        31.73        20.19        24.26        23.74 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV 
       21.73        14.50        21.17        14.73        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A07B TCGA-A8-A07C 
        9.37         8.75        17.98        29.03        43.00        33.99 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P 
        9.99         8.98        24.99        38.01         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A23H TCGA-AC-A2BK 
        0.99        43.00        14.01         0.99         5.72        38.53 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A7VC 
       33.04         2.27        16.57        13.71        13.58         0.03 
TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.12         1.78         1.71         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FX 
        0.33         0.33         7.96         7.59         0.33         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03U TCGA-AO-A0J2 
        0.53         0.33         0.33        61.35        58.95        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       102.58 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J 
      106.78       108.03        64.04        48.36        70.39        26.93 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0TX 
      130.09         2.56       111.32        74.79        13.71        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       65.36        85.97        75.55        61.84        52.77        43.07 
TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 
       17.23        41.82        33.73       104.28        53.36        78.48 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       72.76        93.83        20.38        10.59        77.62       143.38 
TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RE 
       32.78        12.13       176.98        18.77       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      189.01       100.70        89.46       131.21        21.47       186.48 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 
      101.52       139.17        74.99        59.84        20.45        39.55 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
       56.98        51.68        25.71        24.85        44.05        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E6 
       49.05        41.75        48.23        16.27         4.41         9.63 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q 
       31.00        30.35         5.59        23.05         2.01        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EX TCGA-BH-A1F0 
       37.55         7.36        51.16        69.93        49.58        25.81 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       97.48       114.15        72.07        72.07        26.14        38.60 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12P 
       57.83       130.16        18.64         5.26        11.93        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         0.39         2.24         1.87         1.12 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
        1.05         4.11        10.92         0.16        12.03         2.30 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP 
        0.36         0.43         0.03         9.50         0.99        13.02 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 
       11.90        20.88        13.97        14.17        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL 
       17.49        16.50        12.03        12.03        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW 
       19.40        21.83        14.50        16.41         6.35        12.66 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P 
       14.14        16.04        13.05        13.48        47.15        40.96 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A158 
       38.60        31.96        28.60        25.41        27.12        14.79 
TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LB 
       25.05        60.53        53.62        28.50        33.70        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 
       15.45        34.92        26.56        12.85        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A243 
       13.12        39.55        12.59        34.59        23.51        17.06 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OV TCGA-EW-A1OW 
        0.69         1.94        30.18         0.79        25.94        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR 
       29.82         7.86        19.99         6.15        19.96        55.00 
TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       17.49       109.87        79.10        75.02        70.85        72.10 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YL TCGA-LL-A5YO 
       69.30         2.60        11.84        10.62        17.06        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A8F5 TCGA-OL-A5D6 
       14.79        16.08        15.68        14.50        14.73        36.30 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       58.52        36.36        24.72        22.32        20.38        23.47 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UL-AAZ6 
       14.07        28.21         9.93        16.80        15.39        17.03 
TCGA-UU-A93S 
        3.81 

$subtype3
TCGA-5L-AAT0 TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SJ 
       48.56        14.37        43.43        48.10        47.24        13.68 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CV 
      136.73        99.12       114.81        92.48       107.93        98.99 
TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW 
       53.13       134.40        80.28       107.61        72.00        61.94 
TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T6 TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ 
       24.72        44.28        18.90        19.33        48.46        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC 
       20.25        16.47        52.47       107.70        18.15        20.88 
TCGA-A2-A4RY TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A3J1 TCGA-A7-A425 
       21.30        34.29        33.11        29.56        11.28        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E 
       11.97        14.93        14.66        10.72        11.05        19.99 
TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB 
       31.00         9.99        13.02        21.04        10.85        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN 
       55.43        36.99        38.79        50.70        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP 
       14.83        22.19        23.24        18.67        12.26        20.19 
TCGA-AC-A8OS TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AO-A03R TCGA-AO-A0J9 
        2.30         7.17         6.28         0.33        68.75        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A12A 
       50.70        50.86        21.37        26.24        62.04        90.58 
TCGA-AO-A12E TCGA-AO-A1KO TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO 
       57.30        14.73        51.25        48.82        76.11        43.56 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A252 
       76.21        62.14        84.20        76.01        50.96        73.18 
TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       58.92        20.25        62.86        52.11        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IP 
       40.54        16.04        20.45        65.72       112.37       110.93 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AZ TCGA-BH-A0BA 
      140.48       157.41       113.79        58.88        28.50        37.22 
TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       32.02        21.70        61.68        35.67        48.69        27.19 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       48.13        31.17        23.44        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.65        38.47        67.86        47.41        46.19        32.58 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W4 
       37.78        35.51        23.90         5.85        13.61        24.95 
TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1FB TCGA-BH-A1FE 
       42.35         8.81        72.56        42.28       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ 
       36.92        28.14        10.65       109.28         8.94        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A3M7 TCGA-C8-A8HR TCGA-D8-A145 TCGA-D8-A146 
       21.76         9.44         0.03        13.41        13.48        21.14 
TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1XM TCGA-D8-A27I TCGA-D8-A27K 
       18.71        14.01        14.70        17.69        14.43         9.44 
TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A14Q 
        0.76        12.53        33.37        21.67        27.52        38.24 
TCGA-E2-A14U TCGA-E2-A14Z TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 
       43.33        18.51        20.71        11.05        19.56        53.03 
TCGA-E2-A1B5 TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A3DX 
       32.35        37.41        28.44        20.98        54.18        15.72 
TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK 
       35.77        11.90        28.27         0.76        15.72        14.70 
TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PG TCGA-EW-A2FS 
       12.20        13.25        39.78        30.08        34.55        52.73 
TCGA-EW-A2FV TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN 
       25.91       216.76        85.15       110.50        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       72.03        13.55        62.43        13.22         7.10        13.28 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A73Z TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU 
       24.95        11.44         7.46        22.39         2.10        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A6VQ 
       34.92        28.87        65.62        42.77        26.04        19.73 
TCGA-PE-A5DE TCGA-PL-A8LY TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 
       86.96         0.26        14.96        13.84        11.41        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

subtype1 subtype2 subtype3 
    0.16     0.03     0.03 
subtype1 subtype2 subtype3 
  234.28   211.56   216.76 
subtype1 subtype2 subtype3 
  23.610   23.740   29.215 
[1] "0.2 - 234.3 (23.6)" "0.0 - 211.6 (23.7)" "0.0 - 216.8 (29.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      46       42        6        0       178       126         1
  subtype2      19       22        0        1       132        70         0
  subtype3      24       19        3        2        49        52         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         91         22         23       12         0      10
  subtype2         31          6         14        5         0       1
  subtype3         29          1         26        3         1       3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          46       19       24
  STAGE IA         42       22       19
  STAGE IB          6        0        3
  STAGE II          0        1        2
  STAGE IIA       178      132       49
  STAGE IIB       126       70       52
  STAGE III         1        0        1
  STAGE IIIA       91       31       29
  STAGE IIIB       22        6        1
  STAGE IIIC       23       14       26
  STAGE IV         12        5        3
  STAGE TIS         0        0        1
  STAGE X          10        1        3
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1 146 323  60  27
  subtype2  64 202  27  11
  subtype3  67  99  44   2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      146       64       67
  T2      323      202       99
  T3       60       27       44
  T4       27       11        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 248 192  75  30
  subtype2 167  91  27  16
  subtype3  94  71  16  29
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      248      167       94
  N1      192       91       71
  N2       75       27       16
  N3       30       16       29
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1 467  13
  subtype2 262   5
  subtype3 163   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  467   13
  subtype2  262    5
  subtype3  163    3
   clus
vv  subtype1 subtype2 subtype3
  0      467      262      163
  1       13        5        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1 547  11
  subtype2 305   0
  subtype3 213   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  547   11
  subtype2  305    0
  subtype3  213    0
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      547      305      213
  MALE         11        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           410
  subtype2                          1                           266
  subtype3                          0                           100
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             85                   0
  subtype2                              7                   6
  subtype3                            102                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               19
  subtype2                     4                                2
  subtype3                     0                                8
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                 17             27
  subtype2                  0             18
  subtype3                  0              3
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              0        1        0
  INFILTRATING DUCTAL CARCINOMA         410      266      100
  INFILTRATING LOBULAR CARCINOMA         85        7      102
  MEDULLARY CARCINOMA                     0        6        0
  METAPLASTIC CARCINOMA                   0        4        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       19        2        8
  MUCINOUS CARCINOMA                     17        0        0
  OTHER  SPECIFY                         27       18        3
[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"
D7V9, binary
          cls
clus         0   1
  subtype1 156 402
  subtype2  80 225
  subtype3  54 159
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  156  402
  subtype2   80  225
  subtype3   54  159
     clus
vv    subtype1 subtype2 subtype3
  NO       156       80       54
  YES      402      225      159
[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"
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    33                        66
  subtype2                                1    23                        83
  subtype3                                0     5                        23
          vv
clus       WHITE
  subtype1   392
  subtype2   177
  subtype3   176
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  33       23        5
  BLACK OR AFRICAN AMERICAN              66       83       23
  WHITE                                 392      177      176
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
          cls
clus         0   1
  subtype1  25 430
  subtype2   6 256
  subtype3   7 178
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25  430
  subtype2    6  256
  subtype3    7  178
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           25        6        7
  NOT HISPANIC OR LATINO      430      256      178
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 245  37
  subtype2 129  31
  subtype3  84   6
  subtype4 264  23
  subtype5 160  22
  subtype6  45  12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     282      160       90      287      182       57 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      37       31        6       23       22       12 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SQ TCGA-A2-A04N 
      129.14        42.81         9.96        14.27        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0ER TCGA-A2-A0ET 
      121.94        63.12        88.60        75.55        74.40        35.05 
TCGA-A2-A0SU TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 
       54.64        32.55        50.47        17.36        60.72        19.56 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A4S0 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13F 
       17.19       105.34        23.21        38.30        30.61        25.15 
TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.61        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.41        13.02        13.02        53.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z 
        1.02         9.01        32.05        10.98         7.99        45.07 
TCGA-A8-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-A091 TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C 
       40.01        33.01        17.95         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A9 
       49.05        29.98        33.07        25.02        19.04        27.02 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3TN TCGA-AC-A3YJ 
       38.04         2.37        99.35        26.04        14.99        24.79 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
       11.44        17.42         8.22         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FY 
        0.23         2.96         6.44         5.65         7.00         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33         0.30         0.33        95.70        21.40        20.32 
TCGA-AO-A0J8 TCGA-AO-A0JI TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C 
       22.36        50.24        99.25       108.72        98.27        65.56 
TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       28.37        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       15.62        32.91         5.26        42.35        55.86       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24L 
       83.87       114.02        37.81        61.28        50.89        94.22 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0IA 
       87.22        85.35        79.00        54.21        66.15       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RI TCGA-B6-A0RL 
      129.57        50.70       126.12       110.14       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X4 
       78.02       102.77       188.68        79.63       129.57        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-BH-A0AU TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD 
       68.94        43.59        24.53        49.94        42.90        45.83 
TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H6 
       15.68        44.81        24.49        24.43        15.16        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO 
       41.00        52.96        20.38         2.37        16.96         2.50 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES 
       51.32        23.93        26.66        37.74        66.05       113.82 
TCGA-BH-A1F5 TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A204 
       89.16        33.17       122.89        63.35       144.59        83.31 
TCGA-BH-A42T TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X 
       10.52         9.63         9.70        11.77        11.77        12.66 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       12.33        11.34        11.28        10.42         3.25         0.30 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A1JD 
        8.28         9.67        12.20         0.23        13.25        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 
       18.90        18.97        12.20        13.32        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       16.73        27.58        12.39        17.16        15.22        14.73 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y1 
       15.55        15.85        16.31        12.99        15.16         9.93 
TCGA-D8-A27E TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 
       17.42        12.26         8.02        43.00        59.41        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W 
       40.41        37.51        44.68        33.17        33.30        32.02 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15G 
       23.24        19.43        21.04        23.87        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R 
       12.92        19.40         9.04        20.58        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1IG TCGA-E2-A1IK TCGA-E2-A1IN 
       14.07        14.99        33.01        32.78        22.65        22.19 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A56Z TCGA-E2-A570 
       27.42        39.62        19.66        24.59         8.28        30.61 
TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1NG TCGA-E9-A1NI 
       39.72        34.29        34.82        36.82        25.84         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD 
        2.56         3.02         2.76        21.21        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A229 
       34.65        21.27        35.64        34.13        12.53        13.32 
TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A3HO 
       22.75        20.71        27.22        24.56        29.72        26.07 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J1 
       18.41        12.33        23.84        13.81        14.40        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA 
       28.77        29.95        41.13        23.11        18.48        18.90 
TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GM-A2DC TCGA-GM-A2DM TCGA-LL-A442 
       10.52        52.73        22.09        83.34       106.06        10.95 
TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A66H 
       25.05        15.32         2.63        12.36        31.99        26.70 
TCGA-OL-A66O TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-AA11 TCGA-S3-AA12 TCGA-Z7-A8R6 
       17.36        47.01         0.16        13.84        15.35       107.05 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W 
      131.67        20.88        31.79         7.96        39.32       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D1 
       55.43        36.13       107.93        56.81        55.00        34.55 
TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       31.82        27.12        44.88        21.90        21.67        23.77 
TCGA-A2-A25B TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26H TCGA-A7-A4SF TCGA-A7-A56D 
       42.44        26.96        21.90        23.80        17.92        14.73 
TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       10.42         1.02        17.98        31.00        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B 
       43.00        18.97        14.01         9.99        15.06        38.01 
TCGA-A8-A08F TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       33.01        37.05         9.99        31.00        33.01       112.08 
TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09W 
       30.97        12.00        45.07         1.02         8.98         0.99 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A7VC TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.95         5.72        33.04         0.03         9.96         7.36 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        0.16         0.33         7.04         0.33         0.33        12.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AQ-A0Y5 
        5.59        66.77        81.63        71.80       130.09         5.65 
TCGA-AR-A0TW TCGA-AR-A1AT TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A254 TCGA-B6-A0I8 
       98.93        41.82       160.90        89.00        72.76        24.62 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0WW TCGA-B6-A1KN 
       12.13       146.50       189.01       162.05        18.35       139.17 
TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B4 TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BZ 
       68.12       103.63        39.16        53.69        45.57        49.05 
TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J 
       44.02        16.27        23.08        12.89        50.79        20.12 
TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EX 
       90.84        30.28        51.39        69.93        12.00        49.58 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       17.69        31.53        24.66        45.63        72.07        26.14 
TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A137 
       12.66        12.66        12.66         0.39         3.16         4.11 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-C8-A274 TCGA-C8-A8HQ TCGA-D8-A13Y 
        4.08        10.92         2.30         9.53        12.49        11.90 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JJ TCGA-D8-A1JN 
       14.17        17.49        16.50        15.78        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 
       21.01        23.90        21.83        16.54        15.32        14.14 
TCGA-D8-A27N TCGA-D8-A27R TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14V 
        4.80        10.09        34.42        40.11        28.44        34.26 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A2P5 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N9 
       27.12        23.34        16.93        12.85        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A1RB TCGA-E9-A1RF TCGA-E9-A22A 
       36.56        35.24         6.12        32.09         6.58        39.09 
TCGA-E9-A22E TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A2FR TCGA-EW-A423 TCGA-GI-A2C8 
       12.89        29.85         6.15        55.00        10.16         7.40 
TCGA-GM-A2D9 TCGA-JL-A3YX TCGA-LL-A6FP TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5RZ 
       59.57        11.57        22.26        14.07        27.91        22.32 
TCGA-OL-A97C TCGA-S3-A6ZF TCGA-UL-AAZ6 TCGA-WT-AB44 
        8.91        16.50        17.03        29.03 

$subtype3
TCGA-3C-AALK TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR 
       40.14        43.43        47.24       114.81        92.48       107.93 
TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0YK 
       53.13        80.28        72.00        61.94        24.72        19.33 
TCGA-A2-A0YL TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A7-A0CG 
       48.46        16.47       107.70        39.65        21.30        34.29 
TCGA-A7-A13H TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A0A4 TCGA-AC-A23G 
       29.56        11.97        10.72        11.05        13.02        10.85 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3YI 
       55.43        36.99        38.79        16.31        22.19        23.24 
TCGA-AC-A8OS TCGA-AO-A0JB TCGA-AO-A0JJ TCGA-AO-A1KO TCGA-AR-A1AL TCGA-AR-A1AM 
        2.30        50.70        62.04        14.73        48.82        76.11 
TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       84.20        76.01        50.96        52.11        38.17        40.54 
TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-BH-A0AZ 
       20.45       112.37       110.93       140.48       157.41        28.50 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0DO TCGA-BH-A0DP 
       37.22        21.70        61.68        35.67        17.26        15.65 
TCGA-BH-A0E9 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A18M TCGA-BH-A1FH TCGA-BH-A201 
       46.19        13.61        24.95        72.56        36.92        28.14 
TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A3M7 
       10.65       109.28         8.94        18.87        21.76         0.03 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A1IF 
       33.37        21.67        38.24        43.33        20.71        37.41 
TCGA-E2-A1IJ TCGA-E2-A1L6 TCGA-EW-A1J2 TCGA-EW-A1PG TCGA-GM-A3XG TCGA-GM-A5PV 
       28.44        54.18        13.25        34.55        43.73        13.55 
TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-MS-A51U TCGA-OL-A5RV 
       62.43        13.22        13.28        24.95        22.39        34.92 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PL-A8LY TCGA-S3-AA14 TCGA-W8-A86G TCGA-Z7-A8R5 
       19.73        40.11         0.26        14.96        11.41       108.07 

$subtype4
TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SJ 
       11.44        48.56        48.36        14.37        48.10        13.68 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D3 
      136.73        99.12        75.25         5.19        98.99        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0EU 
       25.22       101.72       134.40       107.61        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        20.88        49.48        50.37         7.30        21.14 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A425 
       35.47        37.45        33.11        31.36        11.28        14.70 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07J 
       14.93        13.74        14.66        19.99        18.97        12.00 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09V 
       12.00        31.00        41.98         9.99        50.04        15.02 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A2B8 TCGA-AC-A2FB 
       12.00        19.04        21.04        17.03         1.48        40.57 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3W6 TCGA-AC-A5XS 
       50.70         0.92        32.45        14.83        19.79         1.55 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A049 
       18.67        12.26         1.68        20.19         0.33         0.62 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT 
        7.17         6.28         0.36         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V 
        5.33        80.28        61.35        68.75        47.87        29.13 
TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF 
       26.04        53.03        21.53        50.86        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12G TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       26.24        90.58        57.30        41.62        32.52        19.20 
TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AU 
       73.64        86.66        51.25        43.73        39.98        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24S 
       63.62        62.14        96.89        78.51         2.76        97.84 
TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LO 
       83.77        73.18        58.92       143.21        62.86        39.39 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IN TCGA-B6-A0RG 
       54.74        16.04       149.59        65.72        84.59        68.45 
TCGA-B6-A0RN TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KI 
      172.96        97.48       113.79       129.70        58.88        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B1 
      170.17        85.35        71.15        25.55        46.95        37.74 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B8 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       48.36        56.94        51.58        32.02        18.21        25.71 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DE 
       48.69        27.19        53.95        41.75        48.13        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DS 
       23.44        38.01        22.13        13.91         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E2 TCGA-BH-A0EA TCGA-BH-A0GY 
       38.47        67.86        47.41        14.30        32.58        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HK 
       10.78        37.78        35.51        26.50        23.90         5.85 
TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I 
       36.85        27.25        42.35        44.81         8.81         7.23 
TCGA-BH-A18R TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FB 
       37.55        91.99        82.85        42.28        55.69       120.62 
TCGA-BH-A1FE TCGA-BH-A1FL TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A5J0 
       74.73        55.00       130.16         6.44        20.12        23.51 
TCGA-BH-AB28 TCGA-C8-A132 TCGA-C8-A26W TCGA-C8-A8HR TCGA-D8-A141 TCGA-D8-A145 
        9.44         1.87         0.23        13.41        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1XB 
       21.14        18.71        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 
        9.44        16.41         0.76        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        12.10        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        17.42        11.05        19.56        53.03        32.35 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1IL TCGA-E2-A1IO 
       16.47        17.10        38.30        33.73         3.88        20.98 
TCGA-E2-A1IU TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1QZ 
       11.08         5.52        15.72        32.88        35.77        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A249 
       28.27        34.95        32.09        32.05        41.03         7.13 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW 
        0.72         0.76        15.72        14.70        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       39.72         8.48        18.21        16.57        15.68        25.94 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FV 
       40.41        39.78        52.96        13.94        14.43        25.91 
TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       34.03        23.51       216.76        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XN 
      115.69       101.62        85.35       110.50        38.20        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A5YN 
       72.03        18.12        21.24         7.10        17.06        14.70 
TCGA-LL-A7SZ TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX TCGA-OL-A66J 
       14.70         2.10        58.62        40.08        28.87        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZG 
       41.92        42.77        26.04        64.21        86.96        13.12 
TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       16.93        13.94        52.96        15.35        16.04 

$subtype5
TCGA-A1-A0SB TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
        8.52        28.01        19.20        18.02        78.41        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX 
       87.25        24.79        67.33        33.76        99.19        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
       17.52         8.38        18.21        18.61        31.73        19.20 
TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY 
       10.59        33.93        83.01        29.98        47.31        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       38.37        24.39        35.31        35.67        31.73        20.19 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       24.26        23.74        21.73        14.50        21.17        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R 
       10.29         9.37         8.75        33.99         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW 
       24.99         0.99        38.53         2.27        13.71        13.58 
TCGA-AC-A8OQ TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        1.12         1.71         6.51         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       102.58       106.78       108.03        48.36 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
       70.39        26.93         2.56       111.32        74.79        13.71 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       65.36        85.97        75.55        61.84        52.77        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR 
       17.23        33.73       104.28        78.48        93.83        20.38 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       10.59        77.62       143.38        32.78       176.98       140.88 
TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      211.56        89.46       131.21        21.47       186.48       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
       74.99        59.84        39.55        51.68        24.85        44.05 
TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA 
       11.67        48.23         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 
        2.01        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         1.12         0.16 
TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK 
        0.99        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        12.66        16.04        13.05        13.48        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 
       38.60        31.96        28.60        25.41        14.79        25.05 
TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       60.53        28.50        33.70        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 
        8.75        43.04        15.45        34.92        26.56        12.00 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA 
       39.55        12.59        23.51        17.06         0.69        30.18 
TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB 
        0.79        22.82        29.82        30.08         7.86        19.99 
TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-HN-A2NL 
       19.96        17.49       109.87        70.85        69.30         2.60 
TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 
       11.44        14.79        16.08        15.68        14.73        58.52 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z 
       36.36        20.38        23.47        28.21         9.93        16.80 
TCGA-S3-AA10 TCGA-S3-AA15 
       15.39        13.84 

$subtype6
TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A3XV TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 
       63.29        17.13        32.75        43.00        14.01         0.99 
TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AO-A0J2 TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TX 
       16.57         1.78        32.78        76.77        64.04        64.83 
TCGA-AR-A1AO TCGA-AR-A24U TCGA-AR-A2LH TCGA-B6-A0IK TCGA-B6-A0RS TCGA-BH-A0AW 
       43.56        53.36        20.25        18.77       100.70        20.45 
TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L 
       56.98        31.00        72.07        38.60        57.83        11.93 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HK TCGA-C8-A26X 
       11.77        12.66         2.24         1.05        12.03         0.36 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A143 
        0.43         0.03         9.50        13.02        20.88        14.17 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT TCGA-E2-A14P TCGA-E2-A1B0 
       12.03        12.03        20.12         6.35        40.96        53.62 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E9-A1RH TCGA-E9-A248 TCGA-GM-A2DB TCGA-GM-A2DD 
       40.47        28.90        34.59         1.94        79.10        75.02 
TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-OL-A5D6 
       11.84        10.62        14.47         7.46        14.50        36.30 
TCGA-OL-A5RY TCGA-OL-A66P TCGA-UU-A93S 
       24.72        14.07         3.81 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.16     0.03     0.03     0.23     0.16     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  234.28   189.01   157.41   216.76   211.56   100.70 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.225   22.080   35.295   26.500   24.325   18.770 
[1] "0.2 - 234.3 (23.2)" "0.0 - 189.0 (22.1)" "0.0 - 157.4 (35.3)"
[4] "0.2 - 216.8 (26.5)" "0.2 - 211.6 (24.3)" "0.0 - 100.7 (18.8)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      20       22        5        0        97        72         1
  subtype2       7        8        0        1        50        37         0
  subtype3       7       10        1        1        17        26         0
  subtype4      41       23        3        1        86        61         0
  subtype5      13       15        0        0        86        40         0
  subtype6       1        5        0        0        23        12         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         42         15          7        4         0       6
  subtype2         31          8         11        7         0       2
  subtype3         14          1         12        1         0       0
  subtype4         42          0         22        3         1       5
  subtype5         15          4          5        3         0       1
  subtype6          7          1          6        2         0       0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          20        7        7       41       13        1
  STAGE IA         22        8       10       23       15        5
  STAGE IB          5        0        1        3        0        0
  STAGE II          0        1        1        1        0        0
  STAGE IIA        97       50       17       86       86       23
  STAGE IIB        72       37       26       61       40       12
  STAGE III         1        0        0        0        0        1
  STAGE IIIA       42       31       14       42       15        7
  STAGE IIIB       15        8        1        0        4        1
  STAGE IIIC        7       11       12       22        5        6
  STAGE IV          4        7        1        3        3        2
  STAGE TIS         0        0        0        1        0        0
  STAGE X           6        2        0        5        1        0
[1] 13  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  76 168  27  18
  subtype2  24 109  20  10
  subtype3  26  36  27   1
  subtype4  94 155  37   2
  subtype5  39 122  16   6
  subtype6  18  34   4   3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       76       24       26       94       39       18
  T2      168      109       36      155      122       34
  T3       27       20       27       37       16        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 124 115  32  12
  subtype2  66  46  31  13
  subtype3  38  35   5  12
  subtype4 144  88  29  24
  subtype5 116  49  13   6
  subtype6  21  21   8   8
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0      124       66       38      144      116       21
  N1      115       46       35       88       49       21
  N2       32       31        5       29       13        8
  N3       12       13       12       24        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 249   5
  subtype2 132   7
  subtype3  69   1
  subtype4 232   3
  subtype5 159   3
  subtype6  51   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  249    5
  subtype2  132    7
  subtype3   69    1
  subtype4  232    3
  subtype5  159    3
  subtype6   51    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      249      132       69      232      159       51
  1        5        7        1        3        3        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 283   8
  subtype2 161   2
  subtype3  90   0
  subtype4 288   1
  subtype5 184   0
  subtype6  59   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  283    8
  subtype2  161    2
  subtype3   90    0
  subtype4  288    1
  subtype5  184    0
  subtype6   59    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      283      161       90      288      184       59
  MALE          8        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"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           221
  subtype2                          0                           136
  subtype3                          0                            28
  subtype4                          0                           178
  subtype5                          1                           160
  subtype6                          0                            53
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             24                   0
  subtype2                             15                   0
  subtype3                             56                   0
  subtype4                             93                   1
  subtype5                              1                   5
  subtype6                              5                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               12
  subtype2                     1                                4
  subtype3                     0                                5
  subtype4                     0                                7
  subtype5                     2                                1
  subtype6                     1                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                 15             19
  subtype2                  1              6
  subtype3                  1              0
  subtype4                  0             10
  subtype5                  0             13
  subtype6                  0              0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         221      136       28      178      160
  INFILTRATING LOBULAR CARCINOMA         24       15       56       93        1
  MEDULLARY CARCINOMA                     0        0        0        1        5
  METAPLASTIC CARCINOMA                   0        1        0        0        2
  MIXED HISTOLOGY (PLEASE SPECIFY)       12        4        5        7        1
  MUCINOUS CARCINOMA                     15        1        1        0        0
  OTHER  SPECIFY                         19        6        0       10       13
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          53
  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"
D8V9, binary
          cls
clus         0   1
  subtype1  91 200
  subtype2  33 130
  subtype3  18  72
  subtype4  77 212
  subtype5  57 127
  subtype6  14  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91  200
  subtype2   33  130
  subtype3   18   72
  subtype4   77  212
  subtype5   57  127
  subtype6   14   45
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        91       33       18       77       57       14
  YES      200      130       72      212      127       45
[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"
D8V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    19                        39
  subtype2                                0    14                        18
  subtype3                                0     3                         9
  subtype4                                0     8                        33
  subtype5                                0     5                        61
  subtype6                                1    12                        12
          vv
clus       WHITE
  subtype1   197
  subtype2   105
  subtype3    75
  subtype4   231
  subtype5   109
  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              39       18        9       33       61
  WHITE                                 197      105       75      231      109
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                  12
  BLACK OR AFRICAN AMERICAN              12
  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  12 226
  subtype2   3 126
  subtype3   2  76
  subtype4  15 231
  subtype5   6 155
  subtype6   0  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  226
  subtype2    3  126
  subtype3    2   76
  subtype4   15  231
  subtype5    6  155
  subtype6    0   50
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO           12        3        2       15        6        0
  NOT HISPANIC OR LATINO      226      126       76      231      155       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 253  45
  subtype2 185  22
  subtype3 236  28
  subtype4 240  33
subtype1 subtype2 subtype3 subtype4 
     298      207      264      273 
subtype1 subtype2 subtype3 subtype4 
      45       22       28       33 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO 
      129.14       131.67        42.81        31.79         7.96        28.01 
TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X 
       19.20        18.02        78.41        73.84        87.25        55.43 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 
       99.12        24.79       107.93        55.00        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SX 
       33.76        25.22        79.76        99.19        27.12        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F 
       17.52         8.38        21.90        31.73        19.20        10.59 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3Y0 
       33.93        83.01        29.98        32.75        47.31        38.37 
TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CJ 
       24.39        23.21        26.96        21.90        35.31        30.61 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A3J0 TCGA-A7-A3RF 
       37.45        31.73        20.19        24.26        10.29        13.41 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       14.50        21.17        17.92        12.10        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C 
        8.75        13.02        17.98        53.98         9.01        33.99 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 
       32.05         9.99         8.98        24.99         9.99        18.05 
TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R 
       38.01         9.99         0.99        45.07        25.02         8.98 
TCGA-A8-A0A7 TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62X 
        0.99        38.53        33.04        16.57        11.44        13.71 
TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
       13.58         1.12         0.33         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        9.96         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.59         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XO TCGA-AN-A0XU TCGA-AO-A03R 
        0.33         0.33         0.53        12.33         0.33        68.75 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0JL 
       32.78        21.40        52.18        37.48        20.32        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
      102.58       108.03        64.04        48.36        61.87        70.39 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       26.93         5.65         2.56       111.32        73.64        74.79 
TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ 
       86.66        83.87        85.97        75.55        61.84        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 
       17.23        33.73       160.90       104.28        78.48        93.83 
TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I9 
       20.38        10.59        77.62       143.38        32.78        12.13 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WX 
      176.98       140.88       211.56       100.70        89.46        21.47 
TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      113.79        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG 
       74.99        59.84        25.55        39.55        51.68        24.85 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0E0 
       45.57        11.67        41.75        45.83        48.23         4.41 
TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G 
        9.63        31.00        30.35         5.59        23.05         2.01 
TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       26.66        55.63        37.55         7.36        51.39        51.16 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FJ TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A204 
       97.48       114.15        63.35        72.07        38.60        83.31 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       18.64        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN 
        2.24         1.12         4.11         0.16         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        0.30         0.43         0.03         9.50        12.20         0.99 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA 
       11.90        20.88        13.97        14.17        19.20        16.50 
TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XJ 
       15.78        20.12        20.09        18.58        15.22        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       14.50        19.92        16.41        15.16        12.66        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A14P 
       14.14        16.04        13.05        13.48        10.09        40.96 
TCGA-E2-A14R TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       38.60        32.02        31.96        28.60        18.51        25.41 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 
       14.79        25.05        23.34        60.53        53.62        28.50 
TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       33.70        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 
       43.04        34.92        26.56        12.85        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22G 
       36.56        12.59        32.09        34.59        39.09        23.51 
TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A5FL TCGA-E9-A5UO 
       17.06         1.94        29.72        30.18         0.79        13.81 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH 
       22.82        29.82         7.86        19.99         6.15        19.96 
TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
       55.00        17.49       109.87        79.10        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LL-A5YN 
       72.10        85.35        69.30         2.60        11.84        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79        16.08        15.68        14.70        12.36 
TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
       14.73        36.30        58.52        36.36        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-AA0Z 
       23.47        14.07        28.21         8.91         9.93        16.80 
TCGA-S3-AA10 TCGA-S3-AA12 TCGA-UL-AAZ6 TCGA-UU-A93S 
       15.39        15.35        17.03         3.81 

$subtype2
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A2-A0CK TCGA-A2-A0CO 
       40.14        11.44        48.36         8.52       136.73       114.81 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES 
      107.93        98.99        53.13       134.40       107.61        72.00 
TCGA-A2-A0EW TCGA-A2-A0T6 TCGA-A2-A0YK TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A25A 
       61.94        18.90        19.33        20.25        16.47       107.70 
TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       18.15        20.88        39.65        49.48        34.98        50.37 
TCGA-A2-A4RY TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A4SC 
       21.30        29.56        23.74        11.34        11.28        14.66 
TCGA-A7-A5ZW TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       10.72        21.04        10.85        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        26.04        50.70         0.92         2.27        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A6IV 
       16.31        14.83        22.19        19.79        23.24        18.67 
TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OS TCGA-AO-A0JF TCGA-AO-A12A 
       12.26         0.03        20.19         2.30        21.37        90.58 
TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TY TCGA-AR-A1AJ 
       57.30        14.73        32.52        19.20        55.86        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX 
       51.25        48.82        76.11        43.56        76.21        62.14 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LE TCGA-AR-A2LH 
       84.20         2.76        76.01        50.96       143.21        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0RQ 
       16.04        20.45        65.72       112.37        18.77       140.48 
TCGA-B6-A0RU TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ 
      131.21       170.17        85.35       103.63        71.15        28.50 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE 
       56.94        44.05        35.67        49.05        48.13        31.17 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E9 TCGA-BH-A0EA 
       22.13        17.26        38.47        67.86        46.19        32.58 
TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EO 
       37.78        13.61        24.95         8.81        72.56        91.99 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE 
       42.28        55.69        49.58        25.81       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       36.92        72.07        28.14        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
      109.28         8.94         5.26        18.87        21.76         9.44 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        0.23         0.36         0.03         0.23        13.02        12.49 
TCGA-C8-A8HR TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A27I TCGA-D8-A27L 
       13.41        18.71        14.01        14.70        14.43        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A108 
        4.80         0.76        13.08        21.67        16.18        27.52 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A1B1 TCGA-E2-A1BC 
       47.15        38.24        43.33        20.71        53.03        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1L6 TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E9-A1NE 
       17.10        33.73        54.18        16.93        15.72        35.77 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-EW-A1IW 
       11.90        28.27         0.76        18.41        15.72        12.20 
TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PF TCGA-EW-A1PG 
       13.25        39.78        30.08        18.90        14.43        34.55 
TCGA-EW-A2FV TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN 
       25.91        83.34        85.15        86.96       115.69       101.62 
TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
      110.50        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.43        11.57        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A73Z TCGA-LL-A740 TCGA-MS-A51U 
       24.95        11.44        17.06         7.46        14.50        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66J 
        2.10        40.08        34.92        28.87        24.72        65.62 
TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA15 TCGA-WT-AB41 
       19.73         0.26        16.93        14.96        13.84        52.96 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       15.35        16.04       108.07 

$subtype3
TCGA-5L-AAT0 TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SQ TCGA-A2-A04N 
       48.56         9.96        43.43        47.24        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CT TCGA-A2-A0CU 
      121.94        63.12        92.48        88.60        75.25         5.19 
TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      101.72        80.28        74.40        35.05        34.29        31.82 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 
       24.72        63.29        44.28        20.52        17.46        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YL TCGA-A2-A0YT 
       32.55        25.28        50.47        21.67        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A4RW TCGA-A2-A4S2 TCGA-A7-A0CD 
       23.47        60.72        52.47         7.30        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A26E TCGA-A7-A26H 
       34.29        35.47        33.11        29.79        31.36        23.80 
TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       20.61        10.59        14.70        11.97        14.93        13.74 
TCGA-A7-A56D TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06Y 
       14.73        11.05        10.42        13.02         1.02        26.01 
TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A084 
       17.03        19.99        18.97        18.97         7.99        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
       36.95         0.99        19.96        33.01       112.08        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A0A2 TCGA-A8-A0A4 
        1.02        50.04        33.07         1.02        19.04        13.02 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A3TN TCGA-AC-A3YJ TCGA-AC-A5XS 
       27.02        17.03        99.35        14.99        24.79         1.55 
TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A046 
       17.42         1.68         8.22         1.32         0.23         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
        6.44         5.65         7.00         7.17         6.28         0.33 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L 
        0.33         0.30         0.33         0.33         5.33        80.28 
TCGA-AO-A03T TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD 
       47.87        22.36        53.03        21.53        50.70        72.00 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12B 
       26.24        50.24        62.04        99.25       106.78        98.27 
TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KP TCGA-AQ-A54O TCGA-AR-A0TR 
       65.56        41.62        28.37        82.62        32.91         5.26 
TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A2LK TCGA-AR-A5QM 
      107.24       114.02        50.89        94.22        54.21        54.74 
TCGA-B6-A0I5 TCGA-B6-A0IC TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG 
      149.59        50.70        84.59       110.14       110.93        68.45 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       78.02       172.96       162.05       188.68        79.63        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0BA 
      129.57       129.70       139.17        68.12        24.53        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BS TCGA-BH-A0C1 TCGA-BH-A0DH TCGA-BH-A0DK 
       32.02        18.21        53.95        44.02        38.01        13.91 
TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GZ TCGA-BH-A0HK 
        3.22        15.68        14.30        44.81        10.78         5.85 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
        2.37        16.96        36.85        51.32        27.25        23.93 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18S TCGA-BH-A1F5 
       42.35        44.81        20.12        30.28        66.05        89.16 
TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A42T TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY 
      122.89        55.00        10.52        23.51         9.63         9.70 
TCGA-C8-A12M TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A9FZ TCGA-D8-A145 
       11.77         8.28         9.67         9.53        19.46        13.48 
TCGA-D8-A1JN TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XG TCGA-D8-A1XM 
       20.38        25.74        23.90        12.39        14.73        17.69 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27W TCGA-D8-A3Z5 
       14.24        17.42        13.45         9.44        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 
       18.51         8.02        12.10        43.00        59.41        34.42 
TCGA-E2-A10F TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15G 
       28.87        27.12        21.04        23.87        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S 
       12.92        17.42        19.40        20.58        17.06        14.07 
TCGA-E2-A1B4 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 
       33.01         5.52         8.28        30.61        39.72        34.29 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1R3 TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A295 
       32.88        36.82         2.56         1.12        34.13         0.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1OX 
       12.33        23.84        14.70        14.40        15.39        29.95 
TCGA-EW-A1P3 TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       52.96        34.03        10.16        23.51         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DM TCGA-GM-A3NY TCGA-LD-A66U TCGA-LL-A442 TCGA-LL-A50Y 
      216.76       106.06        38.20        21.24        10.95        25.05 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 
       15.32        22.26         2.63        14.07        27.91        31.99 
TCGA-OL-A5DA TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       58.62        26.70        41.92        42.77        26.04        17.36 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF 
       40.11        47.01        64.21        86.96         0.16        16.50 
TCGA-S3-A6ZG TCGA-S3-AA11 TCGA-S3-AA17 TCGA-W8-A86G TCGA-WT-AB44 TCGA-Z7-A8R6 
       13.12        13.84        13.94        11.41        29.03       107.05 

$subtype4
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN 
       14.37        48.10        14.27        20.88        13.68        39.32 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0SU TCGA-A2-A0SW 
      101.98        36.13        75.55        61.58        54.64        44.88 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0YI TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G4 
       17.13        49.84        49.48        17.36        22.45        19.56 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A7-A0DA TCGA-A7-A13F TCGA-A7-A13G 
       42.44        17.19       105.34        35.67        25.15        23.61 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07B 
       21.73        22.32        53.06        29.03         1.02        43.00 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08I 
       14.01        12.00        10.98        45.07        13.02        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A09E 
       37.05        31.00        43.00        40.01        30.97        49.05 
TCGA-A8-A09K TCGA-A8-A09T TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0AD TCGA-AC-A23C 
       29.98        19.04        14.01        12.00        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AN-A03X TCGA-AN-A049 TCGA-AN-A0AS 
        2.37         5.72         1.48         0.33         0.62         0.33 
TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03U 
        0.33         5.59        61.35        66.77        81.63        58.95 
TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A126 
       29.13        26.04        50.86        76.77        71.80       108.72 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TV 
        0.53        17.79        24.79       130.09        15.62        42.35 
TCGA-AR-A0TX TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AV 
       64.83        43.73        39.98        37.81        41.82        61.28 
TCGA-AR-A1AW TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U 
       63.62        96.89        78.51        87.22        97.84        53.36 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       85.35        83.77        79.00        89.00        73.18        72.76 
TCGA-AR-A255 TCGA-B6-A0I8 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IM 
       58.92        24.62       220.90       129.57       146.50       126.12 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS 
      189.01       234.28        81.17       102.77       157.41        97.48 
TCGA-B6-A1KI TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B4 
       73.51        20.45        46.95        37.74        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       48.36        56.98        51.58        25.71        21.70        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DG 
       48.69        27.19        53.69        49.94        42.90        23.44 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0EI TCGA-BH-A0H0 
       15.65         2.56        47.41        16.27        24.43        15.16 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18I 
       23.90        20.38         2.50        12.89        50.79         7.23 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV 
       90.84        37.74        69.93       113.82        82.85        12.00 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 
       17.69        31.53        24.66        45.63       144.59        26.14 
TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12X 
       57.83       130.16        11.77        12.66        12.66        12.66 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
        0.39         3.16         1.87         1.05         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-D8-A140 
       10.92        11.34        11.28        12.03        10.42        13.25 
TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        21.14        14.17        17.49        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JP TCGA-D8-A1JS 
       12.03        12.03        18.97        20.09        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD 
       13.32        17.79        16.73        27.58        18.15        17.16 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY 
       15.55        15.85        16.31         6.35        12.99        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       15.52         9.93        12.53        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
       40.11        28.44        44.68        33.17        33.30        34.26 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15K TCGA-E2-A15M 
       23.24        19.43        22.82        17.29         9.04        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF 
       13.02        19.56        14.99        32.35        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.78        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LS TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       15.45        34.82        13.48        35.24        25.84         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
       40.24        34.65         6.58        21.27        35.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        22.75        41.03        12.89        20.71 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-EW-A1IX TCGA-EW-A1IY 
        0.69        27.22         7.13        24.56        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        18.90        16.57        15.68        28.77        25.94 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PD 
       29.85        40.41        41.13        23.11        18.48        13.94 
TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW 
       10.52        52.73        22.09 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.03     0.16     0.33 
subtype1 subtype2 subtype3 subtype4 
  211.56   170.17   216.76   234.28 
subtype1 subtype2 subtype3 subtype4 
  22.570   26.040   23.885   24.660 
[1] "0.0 - 211.6 (22.6)" "0.0 - 170.2 (26.0)" "0.2 - 216.8 (23.9)"
[4] "0.3 - 234.3 (24.7)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      14       16        1        0       132        67         0
  subtype2      24       20        1        2        44        56         1
  subtype3      16       25        6        0        88        57         1
  subtype4      35       22        1        1        90        63         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         38          7         13        7         0       3
  subtype2         30          3         22        3         1       0
  subtype3         36         11         19        3         0       8
  subtype4         44          7          8        6         0       3
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          14       24       16       35
  STAGE IA         16       20       25       22
  STAGE IB          1        1        6        1
  STAGE II          0        2        0        1
  STAGE IIA       132       44       88       90
  STAGE IIB        67       56       57       63
  STAGE III         0        1        1        0
  STAGE IIIA       38       30       36       44
  STAGE IIIB        7        3       11        7
  STAGE IIIC       13       22       19        8
  STAGE IV          7        3        3        6
  STAGE TIS         0        1        0        0
  STAGE X           3        0        8        3
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  48 210  31  11
  subtype2  70  93  40   3
  subtype3  65 155  34  15
  subtype4  94 153  23  11
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       48       70       65       94
  T2      210       93      155      153
  T3       31       40       34       23
  T4       11        3       15       11
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 163  87  31  16
  subtype2  86  80  17  23
  subtype3 127  85  29  21
  subtype4 127  97  38  13
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0      163       86      127      127
  N1       87       80       85       97
  N2       31       17       29       38
  N3       16       23       21       13
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 255   7
  subtype2 157   3
  subtype3 217   4
  subtype4 248   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  255    7
  subtype2  157    3
  subtype3  217    4
  subtype4  248    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      255      157      217      248
  1        7        3        4        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1 297   5
  subtype2 207   0
  subtype3 268   2
  subtype4 277   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  297    5
  subtype2  207    0
  subtype3  268    2
  subtype4  277    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE      297      207      268      277
  MALE          5        0        2        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           263
  subtype2                          0                            89
  subtype3                          0                           176
  subtype4                          0                           235
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              8                   5
  subtype2                            102                   0
  subtype3                             63                   0
  subtype4                             18                   1
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     1                                3
  subtype2                     3                                3
  subtype3                     0                               11
  subtype4                     0                               12
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  5             15
  subtype2                  3              7
  subtype3                  8             12
  subtype4                  1             14
D9V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  INFILTRATING CARCINOMA NOS              1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         263       89      176      235
  INFILTRATING LOBULAR CARCINOMA          8      102       63       18
  MEDULLARY CARCINOMA                     5        0        0        1
  METAPLASTIC CARCINOMA                   1        3        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        3       11       12
  MUCINOUS CARCINOMA                      5        3        8        1
  OTHER  SPECIFY                         15        7       12       14
[1] 8 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus         0   1
  subtype1  81 221
  subtype2  34 173
  subtype3  62 208
  subtype4 107 174
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81  221
  subtype2   34  173
  subtype3   62  208
  subtype4  107  174
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        81       34       62      107
  YES      221      173      208      174
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    20                        84
  subtype2                                0    11                        29
  subtype3                                0     9                        40
  subtype4                                1    21                        18
          vv
clus       WHITE
  subtype1   176
  subtype2   161
  subtype3   188
  subtype4   212
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1
  ASIAN                                  20       11        9       21
  BLACK OR AFRICAN AMERICAN              84       29       40       18
  WHITE                                 176      161      188      212
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
          cls
clus         0   1
  subtype1   4 255
  subtype2  11 180
  subtype3  10 208
  subtype4  13 214
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  255
  subtype2   11  180
  subtype3   10  208
  subtype4   13  214
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4       11       10       13
  NOT HISPANIC OR LATINO      255      180      208      214
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 246  43
  subtype2 126  23
  subtype3 219  25
  subtype4 126  11
  subtype5  84   9
  subtype6 113  17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     289      149      244      137       93      130 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      43       23       25       11        9       17 
$subtype1
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK 
      129.14        42.81         9.96        14.27        13.68        31.79 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A0CT 
       63.12       101.98        55.43        36.13        88.60        75.25 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0EO TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T1 
      107.93        34.55        80.28        63.29        44.88        17.13 
TCGA-A2-A0T3 TCGA-A2-A0YC TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV 
       49.84        32.55        21.90        21.67        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3XZ TCGA-A7-A0CJ 
       17.36        42.44        17.19       105.34        50.37        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26J 
       37.45        33.11        25.15        23.61        31.36        20.61 
TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06Y 
       22.32        17.92        10.42        13.02         1.02        26.01 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        18.97        18.97        14.01 
TCGA-A8-A084 TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       15.06        37.05         9.99        31.00        33.01       112.08 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       30.97        17.95        41.98         9.99         9.99        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09X 
       49.05        45.07        33.07        25.02        19.04        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A3YJ 
       19.04        13.02        17.03         0.95         5.72        24.79 
TCGA-AC-A62V TCGA-AC-A7VB TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04D 
       11.44         8.22         0.33         0.33         2.96         1.71 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0XO TCGA-AN-A0XS 
        7.36         0.16         0.33         7.04        12.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 
        5.59        80.28        81.63        29.13        21.40        26.04 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM 
       22.36        21.53        50.70        50.86        76.77        71.80 
TCGA-AO-A125 TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KT TCGA-AQ-A04L 
       99.25        65.56        41.62        82.62        17.79       130.09 
TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AS 
       15.62        73.64        64.83       107.24        83.87        37.81 
TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       41.82        61.28        63.62       160.90        50.89        94.22 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LK 
       83.77        79.00        89.00        73.18        72.76        54.21 
TCGA-B6-A0I8 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IN TCGA-B6-A0IO 
       24.62       129.57        65.72       146.50        84.59       110.14 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW 
       68.45        81.17       172.96        97.48        79.63        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      113.79       129.57        24.53        20.45        25.55        28.50 
TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BS 
       37.74        39.16        56.94        32.02        48.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DK TCGA-BH-A0DX 
       45.57        49.94        41.75        42.90        13.91        47.41 
TCGA-BH-A0DZ TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 TCGA-BH-A0H7 
       16.27        30.35        10.78        15.16        35.51        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN 
       41.00        52.96        26.50        20.38         2.37        16.96 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       12.89        27.25        26.66        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FL 
       82.85        12.00        55.69        31.53        24.66        55.00 
TCGA-BH-A1FM TCGA-BH-A209 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       45.63       130.16        11.77        11.77        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
       12.66         0.39         1.87        12.33        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.03         2.30         0.30         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J8 
       12.20        19.46        11.90        13.25        20.58        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP 
       17.49        16.50        18.15        20.09        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       12.20        18.58        27.58        17.16        15.22        14.73 
TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-E2-A105 TCGA-E2-A109 
       12.99        15.52         9.93        14.14        43.00        46.59 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A152 TCGA-E2-A155 
       40.11        28.44        44.68        33.30        27.12        21.04 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K 
       23.34        20.71        21.63        18.21        17.42         9.04 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.35        38.30        32.78         3.88        22.19        20.98 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A576 TCGA-E2-A9RU 
       27.42        39.62        19.66        40.47        34.29        12.85 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF 
       36.82        13.48        13.12        36.56        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       25.84         9.86        34.95         6.12         3.02         2.76 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B 
       34.65        21.27        34.13        12.53        13.32        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A6HE TCGA-EW-A1IZ TCGA-EW-A1J6 
       12.89        20.71        27.22        15.39        18.21        28.77 
TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P6 TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A2FV 
       25.94        40.41        18.48         6.15        52.73        25.91 
TCGA-EW-A423 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 
       10.16        15.32        14.70         2.63        14.70        12.36 
TCGA-LL-A9Q3 TCGA-OL-A5D8 TCGA-OL-A5RZ TCGA-OL-A66H TCGA-S3-A6ZH TCGA-S3-AA11 
       14.07        31.99        22.32        26.70        16.93        13.84 
TCGA-S3-AA17 
       13.94 

$subtype2
TCGA-3C-AALI TCGA-A1-A0SB TCGA-A1-A0SM TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A0CL 
      131.67         8.52         7.96        18.02        78.41        99.12 
TCGA-A2-A0CY TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0ST TCGA-A2-A0SV 
       55.00        33.76        79.76        31.82        99.19        27.12 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A4RW 
       17.52         8.38        19.20        33.93        32.75         7.30 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26I TCGA-A7-A4SD TCGA-A8-A06R TCGA-A8-A06U 
       26.96        21.90        21.73        14.50        17.98        29.03 
TCGA-A8-A075 TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A097 
       17.03         9.99        18.05        38.01        43.00        12.00 
TCGA-A8-A09K TCGA-A8-A0A7 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5XS TCGA-AC-A6IX 
       29.98         0.99        33.04         2.27         1.55        12.26 
TCGA-AC-A7VC TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        0.03         1.78         9.96         6.51         0.33         0.33 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.53         0.33 
TCGA-AO-A03M TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A1KS 
       61.35        32.78        72.00       102.58        64.04         0.53 
TCGA-AQ-A0Y5 TCGA-AR-A0TT TCGA-AR-A0TY TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX 
        5.65        86.66        55.86        43.56        76.21        62.14 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0RS 
       97.84        53.36        78.48        10.59        12.13       100.70 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0C3 
       39.55        56.98        24.85        44.05        11.67        48.13 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0RX TCGA-BH-A18R TCGA-BH-A18U 
       45.83        48.23        31.00         5.59        37.55        51.39 
TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       51.16        25.81        72.07        72.07        26.14        38.60 
TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 
       57.83        11.93        12.66        12.66         3.16         2.24 
TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A8HP 
        1.05        10.92         3.25         0.36         0.43        13.02 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JG 
       20.88        13.97        14.17        15.78        12.03        12.03 
TCGA-D8-A1JK TCGA-D8-A1XT TCGA-D8-A1XZ TCGA-D8-A27R TCGA-E2-A108 TCGA-E2-A14P 
       20.12         6.35        15.32        10.09        27.52        40.96 
TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A1B0 
       32.02        18.51        25.41        25.05        12.92        53.62 
TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A574 TCGA-E9-A1RF 
       24.59       106.75        43.04        15.45        26.56         6.58 
TCGA-E9-A1RH TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1OY TCGA-EW-A1P1 
       34.59        17.06         1.94         0.79        29.85        39.78 
TCGA-EW-A1P7 TCGA-EW-A1PH TCGA-EW-A2FR TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
       30.08        19.96        55.00       216.76        79.10        75.02 
TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y 
       72.10        11.84        17.06        14.47        14.79        15.68 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OK-A5Q2 TCGA-OL-A5RW TCGA-OL-A66N TCGA-OL-A66P 
        7.46        14.73         2.10        36.36        26.04        14.07 
TCGA-OL-A97C TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-WT-AB44 
        8.91        13.84        17.03         3.81        29.03 

$subtype3
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-A2-A04N TCGA-A2-A0CK TCGA-A2-A0CO 
       40.14        11.44        48.56       104.81       136.73       114.81 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CZ TCGA-A2-A0EM TCGA-A2-A0EP 
       92.48       107.93         5.19        53.13       101.72       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU 
       74.40        72.00        34.29        61.94        24.72        54.64 
TCGA-A2-A0T4 TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G0 TCGA-A2-A1G6 
       20.52        25.28        19.33        48.46        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW 
       52.47       107.70        18.15        20.88        39.65        49.48 
TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A3IZ 
       21.30        21.14        34.29        29.56        23.80        10.59 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC 
       11.28        14.70        11.97        14.93        13.74        14.66 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E TCGA-AC-A2B8 TCGA-AC-A2BM 
       14.73        10.72        11.05        19.99         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OP 
       16.57        19.79        23.24        17.42        18.67        20.19 
TCGA-AC-A8OS TCGA-AN-A0FF TCGA-AN-A0FS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03T 
        2.30         5.65         6.28         0.33         5.33        47.87 
TCGA-AO-A0JI TCGA-AO-A128 TCGA-AO-A1KO TCGA-AQ-A7U7 TCGA-AR-A1AL TCGA-AR-A1AM 
       50.24       106.78        14.73        19.20        48.82        76.11 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       76.01        50.96       143.21        20.25        62.86        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       52.11        38.17        39.39        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A2IU TCGA-B6-A401 
       20.45       112.37        78.02       140.48       170.17        85.35 
TCGA-B6-A40C TCGA-BH-A0BD TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DG 
       71.15        18.21        35.67        49.05        44.02        23.44 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DV TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0W4 
       22.13        17.26        67.86        14.30        46.19        24.95 
TCGA-BH-A0W5 TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FE 
       42.35        72.56        42.28        49.58       120.62        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
      122.89        36.92        28.14        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28         8.94        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A137 TCGA-C8-A26W 
        9.70        18.87        21.76         9.44         4.11         0.23 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
        8.28         9.67         0.03         0.23        12.49        13.41 
TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XJ 
       18.71        14.01        14.70        25.74        23.90        21.83 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I 
       19.92        17.69        14.24        17.42        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
        9.44        16.41         4.80         0.76        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X 
       12.26        33.37        18.51        21.67        16.18        12.10 
TCGA-E2-A107 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15C TCGA-E2-A15L TCGA-E2-A1B1 
       34.42        38.24        43.33        22.82        20.58        53.03 
TCGA-E2-A1L6 TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       54.18        28.90        16.93         5.52        15.72         8.28 
TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RB 
       39.72        32.88        11.90        28.27         2.56        32.09 
TCGA-E9-A1RD TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3X8 
        1.12        39.09         0.72        29.72         0.76        15.72 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1PA TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A3E8 
       14.70        14.40        18.90        14.43        34.55        34.03 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK 
       23.51         7.40        59.57        83.34        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        62.43        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A50Y TCGA-LL-A6FP TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 
       25.05        22.26        14.50        27.91        22.39        36.30 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66J 
       58.62        40.08        34.92        28.87        24.72        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC 
       41.92        42.77        17.36        19.73        40.11        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA14 TCGA-W8-A86G 
       64.21        86.96         0.26        13.12        14.96        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        15.35        16.04       108.07 

$subtype4
TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI 
       48.36        14.37        43.43        48.10        47.24        20.88 
TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0SY 
       39.32        75.55        98.99        61.58       134.40        44.28 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A1FZ TCGA-A7-A0CH 
       17.46        18.90        20.75        49.48        22.45        35.47 
TCGA-A8-A07J TCGA-A8-A08A TCGA-A8-A08Z TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N 
       12.00         0.99        40.01        12.00         1.02         1.02 
TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A6NO TCGA-AN-A03Y 
       12.00        21.04         2.37        10.85         1.68         0.33 
TCGA-AN-A049 TCGA-AN-A0FD TCGA-AN-A0FN TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A03R 
        0.62         6.44         7.17         0.33        66.77        68.75 
TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12E 
       53.03        21.37        62.04       108.72        90.58        57.30 
TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A0U3 TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A1AP 
       32.52         5.26       114.02        51.25        43.73        39.98 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24V TCGA-AR-A255 
       96.89        78.51        84.20         2.76        85.35        58.92 
TCGA-B6-A0I5 TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RH TCGA-B6-A0RO 
      149.59        18.77       126.12       110.93       189.01       162.05 
TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0X0 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 
      102.77       157.41       129.70        73.51       139.17        68.12 
TCGA-B6-A40B TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF 
      103.63        46.95        40.83        48.36        37.22        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0DE TCGA-BH-A0DP 
       21.70        61.68        27.19        53.69        31.17        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0HF 
        2.56        38.47        32.58        24.43        37.78        23.90 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0W7 TCGA-BH-A18F 
        5.85        13.61        36.85        50.79        44.81         8.81 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A1EY TCGA-BH-A1FJ 
        7.23        20.12        90.84        30.28        17.69        63.35 
TCGA-C8-A138 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JE TCGA-D8-A1X7 TCGA-D8-A1XB 
        4.08        13.48        21.14        18.90        16.73        18.15 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XY TCGA-E2-A10B TCGA-E2-A10F 
       15.55        15.85        16.31        16.54        37.51        28.87 
TCGA-E2-A14V TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15J TCGA-E2-A1B4 
       34.26        23.24        19.43        17.29        19.40        33.01 
TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IU 
       17.10        37.41        33.73        28.44        22.65        11.08 
TCGA-E2-A570 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A249 
       30.61        32.09        40.24        35.64        32.05         7.13 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       12.20        39.72         8.48        13.25        16.57        15.68 
TCGA-EW-A1P3 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-S3-A6ZF TCGA-Z7-A8R6 
       52.96        13.94        10.52        16.50       107.05 

$subtype5
TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0YF TCGA-A2-A1FX 
       18.21       121.94        25.22        35.05        50.47        60.72 
TCGA-A2-A1G4 TCGA-A2-A4S0 TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A3IY TCGA-A7-A3J0 
       19.56        23.21        38.30        29.79        11.34        10.29 
TCGA-A7-A3RF TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A07L TCGA-A8-A07P 
       13.41        13.02        53.06         1.02        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08I 
        7.99        45.07        36.95        13.02        19.96        12.00 
TCGA-A8-A091 TCGA-A8-A09R TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A8OR TCGA-AN-A041 
       33.01         8.98        27.02        38.04         1.32         0.23 
TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A0JG TCGA-AO-A12B 
        7.00         0.30         0.33        20.32        26.24        98.27 
TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AQ-A54O TCGA-AR-A0TV TCGA-AR-A24R 
       28.37        61.87        24.79        32.91        42.35        87.22 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0RI TCGA-B6-A0WT TCGA-B6-A0X4 TCGA-B6-A0X5 
      220.90        50.70       234.28       188.68        28.27        68.94 
TCGA-B6-A1KC TCGA-BH-A0B8 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E7 
       43.59        51.58        38.01         3.22        15.68        44.81 
TCGA-BH-A0H6 TCGA-BH-A0HO TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18N TCGA-BH-A18S 
       24.56         2.50        51.32        23.93        37.74        66.05 
TCGA-BH-A1F5 TCGA-BH-A1FR TCGA-BH-A204 TCGA-C8-A12X TCGA-C8-A1HL TCGA-D8-A1JI 
       89.16       144.59        83.31        12.66        10.42        18.97 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XC TCGA-D8-A1XV TCGA-D8-A73W TCGA-E2-A106 
       13.32        17.79        12.39        15.16         8.02        59.41 
TCGA-E2-A10A TCGA-E2-A14S TCGA-E2-A156 TCGA-E2-A1BC TCGA-E9-A1N3 TCGA-E9-A1R7 
       40.41        33.17        23.87        16.47        34.82        21.21 
TCGA-E9-A22D TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO 
       41.03        24.56        18.41        12.33        23.84        13.81 
TCGA-EW-A1J1 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A2FW TCGA-GM-A2DM 
       18.90        29.95        41.13        23.11        22.09       106.06 
TCGA-LL-A442 TCGA-PL-A8LX TCGA-S3-AA12 
       10.95         0.16        15.35 

$subtype6
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 
       28.01        19.20        73.84        87.25        24.79        67.33 
TCGA-A2-A0SX TCGA-A2-A0YM TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       50.43        31.73        10.59        83.01        29.98        47.31 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D 
       34.98        38.37        24.39        35.31        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV 
       20.19        24.26        23.74        21.17        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
        9.37         8.75        33.99         9.99         8.98        24.99 
TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A0FJ 
        0.99        38.53        13.71        13.58         1.12         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 
        7.59         0.33         0.33        58.95        52.18        37.48 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N 
       55.33       108.03        48.36        70.39        26.93         2.56 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      111.32        74.79        85.97        75.55        61.84        52.77 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LR 
       43.07        17.23        33.73       104.28        93.83        20.38 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE 
       77.62       143.38        32.78       176.98       140.88       211.56 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A402 
       89.46       131.21        21.47        58.88       101.52        74.99 
TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0WA TCGA-BH-A18G 
       59.84        51.68         4.41         9.63        23.05         2.01 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A5IZ TCGA-C8-A12V 
       55.63         7.36        97.48       114.15        18.64        12.66 
TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1XK 
        1.12         0.16         0.99        19.20        20.09        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N 
       16.41        12.66        16.04        13.05        13.48        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A158 TCGA-E2-A1AZ TCGA-E2-A1B6 
       38.60        31.96        28.60        14.79        60.53        28.50 
TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N8 
       33.70        18.87       102.61         8.75        34.92        12.00 
TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P4 
       12.59        23.51         0.69        30.18        22.82        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL 
        7.86        19.99        17.49       109.87        70.85        69.30 
TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5S0 TCGA-OL-A66I 
        2.60        11.44        16.08        58.52        20.38        23.47 
TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
       28.21         9.93        16.80        15.39 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.03     0.03     0.33     0.16     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  172.96   216.76   170.17   189.01   234.28   211.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   23.77    19.96    23.03    31.17    24.56    27.47 
[1] "0.0 - 173.0 (23.8)" "0.0 - 216.8 (20.0)" "0.0 - 170.2 (23.0)"
[4] "0.3 - 189.0 (31.2)" "0.2 - 234.3 (24.6)" "0.2 - 211.6 (27.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      18       23        2        0        97        65         1
  subtype2      12        8        1        2        55        31         0
  subtype3      16       27        3        1        62        66         1
  subtype4      26        7        2        0        44        31         0
  subtype5       9        6        1        0        32        23         0
  subtype6       8       12        0        0        64        27         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         48          8         17        7         1       8
  subtype2         23          3          9        6         0       0
  subtype3         39          3         23        1         0       2
  subtype4         11          6          8        3         0       1
  subtype5         17          6          1        1         0       1
  subtype6         10          2          4        1         0       2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          18       12       16       26        9        8
  STAGE IA         23        8       27        7        6       12
  STAGE IB          2        1        3        2        1        0
  STAGE II          0        2        1        0        0        0
  STAGE IIA        97       55       62       44       32       64
  STAGE IIB        65       31       66       31       23       27
  STAGE III         1        0        1        0        0        0
  STAGE IIIA       48       23       39       11       17       10
  STAGE IIIB        8        3        3        6        6        2
  STAGE IIIC       17        9       23        8        1        4
  STAGE IV          7        6        1        3        1        1
  STAGE TIS         1        0        0        0        0        0
  STAGE X           8        0        2        1        1        2
[1] 13  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  69 181  33  12
  subtype2  39  92  15   5
  subtype3  65 127  47   4
  subtype4  52  68  11   8
  subtype5  25  53  12   7
  subtype6  27  90  10   4
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       69       39       65       52       25       27
  T2      181       92      127       68       53       90
  T3       33       15       47       11       12       10
  T4       12        5        4        8        7        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 119 105  40  22
  subtype2  73  41  23  11
  subtype3 110  83  23  25
  subtype4  72  47  10  10
  subtype5  43  40  11   1
  subtype6  86  33   8   4
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0      119       73      110       72       43       86
  N1      105       41       83       47       40       33
  N2       40       23       23       10       11        8
  N3       22       11       25       10        1        4
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1 250   8
  subtype2 124   6
  subtype3 185   1
  subtype4 121   3
  subtype5  84   1
  subtype6 113   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  250    8
  subtype2  124    6
  subtype3  185    1
  subtype4  121    3
  subtype5   84    1
  subtype6  113    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0      250      124      185      121       84      113
  1        8        6        1        3        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"
D10V7, binary
          cls
clus         0   1
  subtype1 294   3
  subtype2 148   3
  subtype3 244   0
  subtype4 137   2
  subtype5  94   3
  subtype6 132   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  294    3
  subtype2  148    3
  subtype3  244    0
  subtype4  137    2
  subtype5   94    3
  subtype6  132    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      294      148      244      137       94      132
  MALE          3        3        0        2        3        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           249
  subtype2                          0                           129
  subtype3                          0                           101
  subtype4                          0                           100
  subtype5                          0                            69
  subtype6                          1                           115
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             22                   1
  subtype2                             10                   0
  subtype3                            131                   0
  subtype4                             25                   0
  subtype5                              2                   0
  subtype6                              1                   5
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               10
  subtype2                     3                                1
  subtype3                     1                                3
  subtype4                     0                                9
  subtype5                     0                                5
  subtype6                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  1             14
  subtype2                  0              8
  subtype3                  3              5
  subtype4                  0              5
  subtype5                 13              8
  subtype6                  0              8
D10V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         249      129      101      100       69
  INFILTRATING LOBULAR CARCINOMA         22       10      131       25        2
  MEDULLARY CARCINOMA                     1        0        0        0        0
  METAPLASTIC CARCINOMA                   0        3        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        1        3        9        5
  MUCINOUS CARCINOMA                      1        0        3        0       13
  OTHER  SPECIFY                         14        8        5        5        8
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              1
  INFILTRATING DUCTAL CARCINOMA         115
  INFILTRATING LOBULAR CARCINOMA          1
  MEDULLARY CARCINOMA                     5
  METAPLASTIC CARCINOMA                   0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          8
[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"
D10V9, binary
          cls
clus         0   1
  subtype1 101 196
  subtype2  41 110
  subtype3  33 211
  subtype4  42  97
  subtype5  30  67
  subtype6  37  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101  196
  subtype2   41  110
  subtype3   33  211
  subtype4   42   97
  subtype5   30   67
  subtype6   37   95
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO       101       41       33       42       30       37
  YES      196      110      211       97       67       95
[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"
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    22                        41
  subtype2                                0    13                        24
  subtype3                                0    12                        39
  subtype4                                0     5                         8
  subtype5                                0     4                         9
  subtype6                                0     5                        50
          vv
clus       WHITE
  subtype1   197
  subtype2   100
  subtype3   189
  subtype4   117
  subtype5    64
  subtype6    70
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                  22       13       12        5        4
  BLACK OR AFRICAN AMERICAN              41       24       39        8        9
  WHITE                                 197      100      189      117       64
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   5
  BLACK OR AFRICAN AMERICAN              50
  WHITE                                  70
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
          cls
clus         0   1
  subtype1   7 227
  subtype2   5 124
  subtype3  10 220
  subtype4   8 108
  subtype5   5  64
  subtype6   3 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  227
  subtype2    5  124
  subtype3   10  220
  subtype4    8  108
  subtype5    5   64
  subtype6    3  114
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            7        5       10        8        5        3
  NOT HISPANIC OR LATINO      227      124      220      108       64      114
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 153  24
  subtype2 118  16
  subtype3  92   6
  subtype4  95  14
  subtype5 113  11
subtype1 subtype2 subtype3 subtype4 subtype5 
     177      134       98      109      124 
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       16        6       14       11 
$subtype1
TCGA-3C-AAAU TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0T3 TCGA-A2-A1FW 
      129.14        39.32        75.55        61.58        49.84        17.36 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A7-A13F TCGA-A7-A13G 
       22.45        20.25        19.56        42.44        25.15        23.61 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A7VB 
       10.29        13.41         0.95         2.37         5.72         8.22 
TCGA-AO-A03V TCGA-AO-A12A TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       29.13        90.58        28.37        82.62         0.53        17.79 
TCGA-AQ-A1H2 TCGA-AR-A0TY TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV 
       15.62        55.86        51.25        39.98        41.82        61.28 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24V 
      160.90        94.22        96.89        78.51        87.22        85.35 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0RH 
       83.77        79.00        89.00        73.18        58.92       189.01 
TCGA-B6-A1KN TCGA-BH-A0AU TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS 
      139.17        24.53        56.98        48.69        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HN 
       45.57        45.83        23.44        35.51        52.96        16.96 
TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1EN 
        7.23        90.84        26.66        37.74        66.05        69.93 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 
      113.82        12.00        49.58        17.69        89.16        24.66 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 TCGA-C8-A12N 
       55.00        45.63       144.59        26.14        83.31        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A138 
       12.66        12.66        12.66        12.66         1.87         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34        11.28        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
        2.30         3.25        12.20        11.90        13.25        20.58 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI 
       14.17        17.49        15.78        18.15        18.90        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.09        21.01        12.20        18.58        17.79        16.73 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XO TCGA-D8-A1XR 
       27.58        12.39        17.16        15.22        15.55        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        12.99        15.16        16.54        15.52         9.93 
TCGA-D8-A27V TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A152 
       12.53        40.41        44.68        33.30        32.02        27.12 
TCGA-E2-A154 TCGA-E2-A15C TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K 
       19.43        22.82        18.21        12.92        17.42         9.04 
TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG 
       13.02        17.06        14.99        32.35        38.30        32.78 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 
        3.88        22.19        20.98        11.08        39.62        19.66 
TCGA-E2-A1LB TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       40.47        34.82        13.48        35.77        35.24        25.84 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         6.12         3.02         2.76        21.21        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 
       40.24        34.65         6.58        21.27        35.64        12.53 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
       13.32        22.75        41.03        12.89        20.71        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 
        7.13        24.56         8.48        18.90        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P6 
       28.77        25.94        29.85        40.41        41.13        18.48 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-OL-A5RZ 
       52.73        22.09        22.32 

$subtype2
TCGA-3C-AALI TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT 
      131.67        87.25        99.12        19.20        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0DA 
       29.98        47.31        38.37        24.39        26.96        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A7-A6VV 
       31.73        20.19        21.73        14.50        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW 
        9.37         8.75        38.53        16.57        13.71        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A0AT TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
        0.03         1.12         0.33        48.36        61.87        70.39 
TCGA-AR-A0TS TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
       74.79        75.55        61.84        52.77        43.07        17.23 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 
       63.62        33.73       104.28        97.84        53.36        78.48 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A402 
       72.76        93.83        10.59        77.62       101.52        74.99 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A18R TCGA-BH-A18V 
       24.85        44.05        11.67        48.23        37.55        51.16 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L 
       25.81        97.48        72.07       130.16        18.64        11.93 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A278 
       12.66         2.24         1.12         1.05         0.16         9.50 
TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JK 
        0.99        13.02        14.17        19.20        12.03        20.12 
TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XZ 
       20.09        14.50        16.41         6.35        12.66        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R 
       14.14        16.04        13.48        47.15        40.96        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ 
       31.96        28.60        25.41        25.05        11.05        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH 
       53.62        28.50        33.70        27.42        24.59       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
      102.61         8.75        15.45        34.92        26.56        12.85 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 
       12.00        13.12        12.59        34.59        23.51         0.69 
TCGA-E9-A248 TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 
        1.94        30.18        18.21        22.82        29.82        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL 
       19.99         6.15        17.49       109.87        70.85        69.30 
TCGA-HN-A2NL TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
        2.60        11.44        14.47        14.79        16.08        15.68 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ 
       36.36        20.38        23.47        14.07        28.21         9.93 
TCGA-S3-AA0Z TCGA-S3-AA10 
       16.80        15.39 

$subtype3
TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A2-A1FV 
       42.81        40.14        48.56        48.36         9.96        23.47 
TCGA-A2-A1FX TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
       60.72         7.30        21.30        23.21        21.14        21.90 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        14.93        13.74        14.66        17.92        14.73 
TCGA-A7-A5ZX TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OP 
       11.05         1.55        11.44        17.42         1.68        20.19 
TCGA-AC-A8OR TCGA-AQ-A54O TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A408 
        1.32        32.91        54.74        16.04        20.45        68.12 
TCGA-BH-A0DO TCGA-BH-A0HL TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
       17.26         2.37        10.52       109.28         8.94        23.51 
TCGA-BH-A8FY TCGA-BH-AB28 TCGA-C8-A9FZ TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q 
        9.70         9.44        19.46        33.37        21.67        38.24 
TCGA-E2-A14S TCGA-E2-A15F TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 
       33.17        21.63         8.28        30.61        39.72        34.29 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A3E8 
       23.84        14.70        13.81        14.40        15.39        34.03 
TCGA-EW-A424 TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       23.51        43.73        72.03        13.55        18.12        62.43 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       21.24        13.28        10.95        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.70        22.26         2.63        14.07        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       28.87        24.72        26.70        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-AA11 
       26.04        47.01        64.21        86.96         0.16        13.84 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       15.35        13.94        17.03        52.96        29.03        15.35 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

$subtype4
TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A2-A04W 
       11.44         8.52        14.37        48.10        20.88       101.98 
TCGA-A2-A0CV TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A1G6 TCGA-A7-A26E TCGA-A7-A26G 
       98.99       107.61        72.00        16.47        31.36        23.74 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A4SE TCGA-A7-A5ZW TCGA-AC-A23G TCGA-AC-A2B8 
       20.61        11.34        21.17        10.72        10.85         1.48 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A6IV TCGA-AC-A6IX 
       55.43        36.99         2.27        23.24        18.67        12.26 
TCGA-AC-A8OS TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A1AL TCGA-AR-A1AN 
        2.30        14.73        32.52        19.20        48.82        43.73 
TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A24O TCGA-AR-A24P TCGA-B6-A0IH TCGA-B6-A0WS 
       43.56        76.21        84.20         2.76       112.37        97.48 
TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BQ TCGA-BH-A0C3 
       73.51        28.50        46.95        48.36        27.19        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E9 
       42.90        31.17        22.13        38.47        47.41        46.19 
TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU 
       24.43        37.78         8.81        72.56        91.99        42.28 
TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FU 
       55.69        31.53       120.62        74.73        36.92        72.07 
TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A6R9 TCGA-BH-A8G0 TCGA-C8-A8HR 
       28.14        57.83        10.65         5.26        21.76        13.41 
TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU 
       20.88        13.48        21.14        18.71        14.01        14.70 
TCGA-D8-A1XB TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A14U TCGA-E2-A153 TCGA-E2-A15D 
       18.15        16.18        12.10        43.33        23.24        17.29 
TCGA-E2-A15E TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IH 
       20.71        53.03        33.01        16.47        17.10        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1QZ TCGA-E9-A227 
       28.44        22.65        54.18        15.72        11.90        32.05 
TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1J2 TCGA-EW-A1P1 
       15.72         0.79        12.20        39.72        13.25        39.78 
TCGA-EW-A1PD TCGA-EW-A1PG TCGA-EW-A2FR TCGA-GM-A3XN TCGA-LD-A9QF TCGA-LL-A440 
       13.94        34.55        55.00        66.38        10.62        24.95 
TCGA-LL-A740 TCGA-OL-A97C TCGA-PL-A8LY TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G 
       14.50         8.91         0.26        14.96        13.84        11.41 
TCGA-XX-A89A 
       16.04 

$subtype5
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A25A TCGA-A2-A25D 
      136.73       114.81       107.93       107.93       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        39.65        32.75        49.48        34.98        50.37 
TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 
       33.11        29.56        23.80        22.32        10.59        11.28 
TCGA-A7-A6VX TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       10.42        99.35        40.57        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       33.04         0.92        32.45        16.31        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AR-A1AM TCGA-AR-A2LH TCGA-AR-A2LJ 
       14.99        19.79        24.79        76.11        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        52.11        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 
       20.38       170.17        85.35       103.63        71.15        56.94 
TCGA-BH-A0E2 TCGA-BH-A0W7 TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A6R8 
       14.30        44.81        38.60         6.44        20.12         9.63 
TCGA-BH-A8FZ TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       18.87         3.16         4.11         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 
        0.43         8.28         9.67         9.53         0.03         0.03 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A1X9 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H 
        0.23        12.49        23.90        17.42        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A73W TCGA-E2-A15P TCGA-E2-A1LE 
       13.08        12.26        18.51         8.02        19.56        28.90 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E9-A1R0 TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A22A 
       16.93         5.52        28.27         1.12        34.13        39.09 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-EW-A1PA TCGA-EW-A2FV 
        0.72        29.72         0.76        18.41        18.90        25.91 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U 
       85.35       110.50        38.20        11.84        11.57        13.22 
TCGA-LD-A7W5 TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A6VQ TCGA-OL-A6VR 
        7.10         7.46        14.70        12.36        19.73        40.11 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UU-A93S 
       16.50        13.12        16.93         3.81 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.53     0.03     0.16     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  189.01   131.67   109.28   120.62   216.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  22.090   23.950   21.650   23.240   20.315 
[1] "0.5 - 189.0 (22.1)" "0.0 - 131.7 (24.0)" "0.2 - 109.3 (21.6)"
[4] "0.3 - 120.6 (23.2)" "0.0 - 216.8 (20.3)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      20       17        1        1        65        39         0
  subtype2      10        7        0        0        65        28         0
  subtype3       5       12        3        1        25        22         0
  subtype4      15        8        0        0        31        29         0
  subtype5      12        7        0        1        33        37         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         26          4          5        1       1
  subtype2         18          3          3        0       0
  subtype3         14          1         13        3       0
  subtype4         14          2          7        1       1
  subtype5         16          3         12        2       0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          20       10        5       15       12
  STAGE IA         17        7       12        8        7
  STAGE IB          1        0        3        0        0
  STAGE II          1        0        1        0        1
  STAGE IIA        65       65       25       31       33
  STAGE IIB        39       28       22       29       37
  STAGE III         0        0        0        0        2
  STAGE IIIA       26       18       14       14       16
  STAGE IIIB        4        3        1        2        3
  STAGE IIIC        5        3       13        7       12
  STAGE IV          1        0        3        1        2
  STAGE X           1        0        0        1        0
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  60 101  13   6
  subtype2  27  95   9   5
  subtype3  23  55  19   2
  subtype4  42  51  14   2
  subtype5  29  68  24   4
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       60       27       23       42       29
  T2      101       95       55       51       68
  T3       13        9       19       14       24
  T4        6        5        2        2        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 85 67 19  6
  subtype2 81 35 17  3
  subtype3 42 34  7 13
  subtype4 48 43 10  7
  subtype5 56 43 11 14
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       85       81       42       48       56
  N1       67       35       34       43       43
  N2       19       17        7       10       11
  N3        6        3       13        7       14
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
          cls
clus         0   1
  subtype1 157   1
  subtype2 109   0
  subtype3  55   3
  subtype4  84   1
  subtype5 100   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  157    1
  subtype2  109    0
  subtype3   55    3
  subtype4   84    1
  subtype5  100    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      157      109       55       84      100
  1        1        0        3        1        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus         0   1
  subtype1 177   4
  subtype2 135   1
  subtype3  97   2
  subtype4 108   1
  subtype5 125   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  177    4
  subtype2  135    1
  subtype3   97    2
  subtype4  108    1
  subtype5  125    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      177      135       97      108      125
  MALE          4        1        2        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           146
  subtype2                          1                           120
  subtype3                          0                            39
  subtype4                          0                            62
  subtype5                          0                            61
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             12                   0
  subtype2                              2                   5
  subtype3                             52                   0
  subtype4                             34                   0
  subtype5                             54                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               10
  subtype2                     2                                1
  subtype3                     0                                2
  subtype4                     2                                2
  subtype5                     0                                1
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  6              7
  subtype2                  0              5
  subtype3                  4              2
  subtype4                  1              8
  subtype5                  4              5
D11V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         146      120       39       62       61
  INFILTRATING LOBULAR CARCINOMA         12        2       52       34       54
  MEDULLARY CARCINOMA                     0        5        0        0        0
  METAPLASTIC CARCINOMA                   0        2        0        2        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        1        2        2        1
  MUCINOUS CARCINOMA                      6        0        4        1        4
  OTHER  SPECIFY                          7        5        2        8        5
[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"
D11V9, binary
          cls
clus         0   1
  subtype1  66 115
  subtype2  41  95
  subtype3   4  95
  subtype4  23  86
  subtype5  17 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66  115
  subtype2   41   95
  subtype3    4   95
  subtype4   23   86
  subtype5   17  108
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        66       41        4       23       17
  YES      115       95       95       86      108
[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"
D11V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                        11   150
  subtype2    10                        50    74
  subtype3     1                        37    59
  subtype4     4                        13    90
  subtype5    16                        23    84
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20       10        1        4       16
  BLACK OR AFRICAN AMERICAN       11       50       37       13       23
  WHITE                          150       74       59       90       84
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
          cls
clus         0   1
  subtype1   8 166
  subtype2   3 126
  subtype3   4  87
  subtype4   7  95
  subtype5   6 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  166
  subtype2    3  126
  subtype3    4   87
  subtype4    7   95
  subtype5    6  117
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            8        3        4        7        6
  NOT HISPANIC OR LATINO      166      126       87       95      117
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 254  41
  subtype2 220  17
  subtype3  97  13
subtype1 subtype2 subtype3 
     295      237      110 
subtype1 subtype2 subtype3 
      41       17       13 
$subtype1
TCGA-3C-AAAU TCGA-5T-A9QA TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0T3 TCGA-A2-A1FV 
      129.14         9.96        87.25        99.12        49.84        23.47 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       17.36        19.20        19.56        42.44        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S0 
       29.98        32.75        47.31        34.98        38.37        23.21 
TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       26.96        35.67        31.73        20.19        25.15        23.61 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SF 
       23.74        21.73        10.29        13.41        14.50        17.92 
TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A23C TCGA-AC-A23H 
       12.10        10.29         9.37         8.75         0.95         5.72 
TCGA-AC-A2BK TCGA-AC-A3YJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A7VB TCGA-AC-A8OR 
       38.53        24.79        13.71        13.58         8.22         1.32 
TCGA-AN-A0AT TCGA-AO-A03V TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ 
        0.33        29.13        48.36        28.37        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A1AH 
       70.39         0.53        15.62        74.79        55.86        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       61.84        52.77        51.25        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY 
       17.23        41.82        76.21        61.28        63.62        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
      160.90        94.22        84.20       104.28        87.22        97.84 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       53.36        83.77        79.00        89.00        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A1KF 
       72.76        58.92        93.83        20.38        77.62       101.52 
TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AU TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL 
      139.17        74.99        24.53        56.98        24.85        44.05 
TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C3 
       48.69        53.69        53.95        45.57        11.67        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HL 
       42.90        45.83        48.23        35.51        52.96         2.37 
TCGA-BH-A0HN TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R 
       16.96         8.81        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-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FL 
       49.58        25.81        89.16        97.48        24.66        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 
       45.63        72.07       144.59        72.07        26.14        83.31 
TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A8FY TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12Q 
      130.16        18.64         9.70        11.93        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.16         2.24         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.12         1.05        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A278 
        0.16        12.03        10.42         2.30         3.25         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A143 
       12.20         0.99        19.46        11.90        13.25        14.17 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JI 
       19.20        14.17        17.49        15.78        12.03        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-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        15.85         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27V 
       15.52         9.93        14.14        17.42        16.04        12.53 
TCGA-E2-A10A TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       40.41        47.15        40.96        38.60        33.17        33.30 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 
       32.02        31.96        28.60        25.41        27.12        25.05 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O 
       20.71        12.92        17.42         9.04        11.05        13.02 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 
       17.06        14.99        60.53        53.62        32.35        28.50 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1L9 
       38.30        32.78        33.70         3.88        27.42        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS 
       24.59        40.47       106.75       102.61         8.75        15.45 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.92        26.56        34.82        13.48        12.00        13.12 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       12.59        35.77        35.24        34.95         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
        2.76        21.21        32.09        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       34.59        12.53        22.75        41.03        23.51        20.71 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
        0.69        27.22        24.56        18.41        30.18        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 
       13.81        14.40        18.21        18.90        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        22.82        29.85        40.41        41.13 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FS 
       29.82        18.48        30.08        19.99         6.15        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DM TCGA-GM-A3XL 
       25.91        22.09        17.49       109.87       106.06        69.30 
TCGA-HN-A2NL TCGA-LL-A442 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-OL-A5RW 
        2.60        10.95        14.47        14.79        15.68        36.36 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LX 
       22.32        20.38        23.47        14.07        28.21         0.16 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-S3-AA17 TCGA-UL-AAZ6 
        9.93        16.80        15.39        15.35        13.94        17.03 
TCGA-UU-A93S 
        3.81 

$subtype2
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0EP TCGA-A2-A1FX 
      136.73       114.81       107.93       107.93       107.61        60.72 
TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ 
      107.70        18.15        20.88        39.65        49.48        50.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0DB 
        7.30        24.39        21.30        21.14        21.90        33.11 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       29.56        31.36        23.80        20.61        22.32        10.59 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SE 
       11.28        14.70        14.93        13.74        14.66        21.17 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-AC-A23G TCGA-AC-A2BM 
       14.73        10.72        11.05        10.42        10.85        99.35 
TCGA-AC-A2FB TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       40.57        38.79        26.04        50.70        33.04         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27        32.45        16.31        14.83        22.19        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       16.57        19.79        23.24         1.55        11.44        17.42 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS 
       12.26         1.68         0.03        20.19         1.12         2.30 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       32.91        19.20        76.11        20.25        62.86        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
       66.15        52.11        38.17        39.39        40.54        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       16.04        20.45        10.59       170.17        85.35        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0E2 TCGA-BH-A203 
      103.63        71.15        56.94        17.26        14.30        38.60 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28         8.94 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26        18.87        21.76         9.44 
TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        4.11         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.67         9.53         0.03         0.03         0.23        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A1X9 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       12.49        13.41        23.90        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A14O TCGA-E2-A14U TCGA-E2-A15F TCGA-E2-A1LE 
        8.02        12.10        44.68        43.33        21.63        28.90 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 
       16.93         5.52        15.72         8.28        30.61        39.72 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1R0 TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A22A 
       34.29        12.85        28.27         1.12        34.13        39.09 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL 
        0.72        29.72         0.76        15.72        14.70         0.79 
TCGA-E9-A6HE TCGA-EW-A1PA TCGA-EW-A2FR TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 
       15.39        18.90        55.00        34.03        23.51         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        85.15        86.96       115.69       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       18.12        62.43        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y 
        7.10        13.28        10.62        24.95        11.44        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        15.32        14.70        22.26         2.63        16.08 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        14.70        12.36        14.07        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L 
       34.92        28.87        24.72        26.70        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       26.04        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 
       86.96         0.26        16.50        13.12        16.93        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       14.96        13.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

$subtype3
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W 
        8.52        14.37        48.10        20.88        39.32       101.98 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES TCGA-A2-A1FZ TCGA-A2-A1G0 
       75.55        98.99        61.58        72.00        22.45        20.25 
TCGA-A2-A1G6 TCGA-A7-A3IY TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG 
       16.47        11.34         2.37         1.48        55.43        36.99 
TCGA-AC-A6IV TCGA-AO-A12A TCGA-AO-A1KO TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AR-A1AL 
       18.67        90.58        14.73        17.79        32.52        48.82 
TCGA-AR-A1AN TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24V TCGA-B6-A0IH 
       43.73        96.89        78.51         2.76        85.35       112.37 
TCGA-B6-A0RH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 
      189.01        97.48        73.51        28.50        46.95        48.36 
TCGA-BH-A0BQ TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DX 
       27.19        31.17        23.44        22.13        38.47        47.41 
TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18M 
       46.19        24.43        37.78        44.81         7.23        72.56 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE 
       91.99        42.28        17.69        31.53       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A208 TCGA-C8-A12N TCGA-C8-A138 TCGA-D8-A13Z 
       36.92        28.14        57.83        11.77         4.08        20.88 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        13.48        21.14        18.71        18.15        18.90 
TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XB TCGA-D8-A1XO TCGA-D8-A1XS 
       14.01        21.01        14.70        18.15        15.55        16.31 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-E2-A14Q TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15C 
       12.99        16.54        38.24        23.24        19.43        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC 
       17.29        18.21        19.56        53.03        33.01        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       17.10        33.73        28.44        22.65        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1RC 
       11.08        54.18        39.62        25.84        11.90        40.24 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A249 
       35.64        32.05        13.32        12.89         1.94         7.13 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PD 
       12.20        39.72         8.48        13.25        39.78        13.94 
TCGA-EW-A1PG TCGA-OL-A66J 
       34.55        65.62 

subtype1 subtype2 subtype3 
    0.16     0.03     1.48 
subtype1 subtype2 subtype3 
  160.90   216.76   189.01 
subtype1 subtype2 subtype3 
  23.610   20.190   23.935 
[1] "0.2 - 160.9 (23.6)" "0.0 - 216.8 (20.2)" "1.5 - 189.0 (23.9)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      27       22        1        1       125        66         0
  subtype2      16       19        3        2        60        63         2
  subtype3      19       10        0        0        34        26         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         42          7          7        2       1
  subtype2         35          5         29        3       0
  subtype3         11          1          4        2       1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          27       16       19
  STAGE IA         22       19       10
  STAGE IB          1        3        0
  STAGE II          1        2        0
  STAGE IIA       125       60       34
  STAGE IIB        66       63       26
  STAGE III         0        2        0
  STAGE IIIA       42       35       11
  STAGE IIIB        7        5        1
  STAGE IIIC        7       29        4
  STAGE IV          2        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  77 189  25  11
  subtype2  57 127  48   5
  subtype3  47  54   6   3
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       77       57       47
  T2      189      127       54
  T3       25       48        6
  T4       11        5        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 158  97  35   8
  subtype2 103  80  21  30
  subtype3  51  45   8   5
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      158      103       51
  N1       97       80       45
  N2       35       21        8
  N3        8       30        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 254   2
  subtype2 161   3
  subtype3  90   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  254    2
  subtype2  161    3
  subtype3   90    2
   clus
vv  subtype1 subtype2 subtype3
  0      254      161       90
  1        2        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 299   4
  subtype2 235   2
  subtype3 108   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  299    4
  subtype2  235    2
  subtype3  108    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      299      235      108
  MALE          4        2        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           248
  subtype2                          0                            99
  subtype3                          0                            81
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             15                   5
  subtype2                            121                   0
  subtype3                             18                   0
          vv
clus       METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                     0                               10
  subtype2                     4                                2
  subtype3                     0                                4
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  9             15
  subtype2                  5              6
  subtype3                  1              6
D12V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         248       99       81
  INFILTRATING LOBULAR CARCINOMA         15      121       18
  MEDULLARY CARCINOMA                     5        0        0
  METAPLASTIC CARCINOMA                   0        4        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        2        4
  MUCINOUS CARCINOMA                      9        5        1
  OTHER  SPECIFY                         15        6        6
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
          cls
clus         0   1
  subtype1  95 208
  subtype2  19 218
  subtype3  37  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95  208
  subtype2   19  218
  subtype3   37   73
     clus
vv    subtype1 subtype2 subtype3
  NO        95       19       37
  YES      208      218       73
[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"
D12V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    27                        61   213
  subtype2    18                        67   147
  subtype3     6                         6    97
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           27       18        6
  BLACK OR AFRICAN AMERICAN       61       67        6
  WHITE                          213      147       97
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
          cls
clus         0   1
  subtype1  13 275
  subtype2   9 218
  subtype3   6  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  275
  subtype2    9  218
  subtype3    6   98
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        9        6
  NOT HISPANIC OR LATINO      275      218       98
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
