[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSARC-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/SARC-TP/11541674/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/11589723/SARC-TP.mergedcluster.txt"

nPatients in clinical file=157, in cluster file=261, common to both=157
[1]   8 157
[1] "CN_CNMF"
[1] 3
 1  2  3  4  5  6  7 
18 34 27 33 22 21  1 
 1  2  3  4  5  6 
18 34 27 33 22 21 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
25 25 42 18 15 22  5 
 1  2  3  4  5  6  7 
25 25 42 18 15 22  5 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
37 56 33 29 
 1  2  3  4 
37 56 33 29 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
26 11 39 21 30 19  9 
 1  2  3  4  5  6  7 
26 11 39 21 30 19  9 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
67 21 67 
 1  2  3 
67 21 67 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
50 18 76 11 
 1  2  3  4 
50 18 76 11 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
50 44 20 
 1  2  3 
50 44 20 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
10 20 30 14  8 12  8 12 
 1  2  3  4  5  6  7  8 
10 20 30 14  8 12  8 12 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 157 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62         1163           NA         1116           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1802          960         1294         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          261 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1809         1666           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3289          520          610          458          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1952           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
         828          455          805         2212          763          380 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
         349         2009          713          881           63          541 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
         658           NA           NA         2017          716           NA 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
        1006         1085          801           NA           NA           14 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
           3           NA            2          618            2            2 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
         818           NA          126           NA          729            3 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        1257          298           NA          650          272           98 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
          42          217           NA           NA          966           NA 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
        4362         3555           NA         2229           NA          688 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
         191           NA           NA         2181         1107          830 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
         356          160          118           72           15          173 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
         136          337          476            3          124         2297 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
          NA           NA           NA           NA           NA          153 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
         236           56           NA           NA           NA          553 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
         639         5324         2841         1688           NA           22 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
          NA          200          154          402           22           NA 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
          NA         2212           NA           NA           NA           NA 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
          NA         1548          525           NA          826          259 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
         476          254          268          996          749          329 
TCGA-X9-A971 
         376 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=101,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 157 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=54, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 10  8
  subtype2 22 12
  subtype3 15 11
  subtype4 26  7
  subtype5 15  7
  subtype6 15  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      18       34       26       33       22       21 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8       12       11        7        7        6 
$subtype1
TCGA-DX-A1L1 TCGA-DX-A2IZ TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A8BX TCGA-DX-AATS 
       46.68         8.58        14.99        28.80        19.43         1.15 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-K1-A42W TCGA-LI-A67I TCGA-MJ-A68H 
        8.94         3.22        25.22        27.29         5.26         4.47 
TCGA-N1-A6IA TCGA-QQ-A5V9 TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-WK-A8XX TCGA-X6-A7WC 
        4.08        46.82        93.40        10.52        38.27        27.16 

$subtype2
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       31.56        42.54        76.41        66.87        27.81        60.30 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       59.47        54.77         9.04        17.75         4.54        44.45 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A7EF TCGA-HB-A2OT TCGA-IS-A3K8 
       28.96        17.79        16.18        21.30        26.89       116.88 
TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DN 
       36.39         2.37         5.69        11.08        15.65        38.63 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG TCGA-RN-A68Q 
        5.03         1.84        48.59        21.01        55.50         0.72 
TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 
       13.22         4.80        41.49        10.82 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LU 
       74.66         5.26         6.28         9.70        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6BH 
      108.13        17.10        20.05        15.06        12.26        21.63 
TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-LI-A9QH TCGA-QQ-A5VC TCGA-SG-A6Z7 
        0.46         4.57        37.12         3.88        18.18         3.88 
TCGA-WK-A8XO TCGA-X6-A8C4 
       11.93         8.81 

$subtype4
TCGA-DX-A3UA TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       10.68         9.73        27.22        14.96        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A8BO TCGA-FX-A3NJ TCGA-FX-A3RE 
       12.49        11.47        23.44        26.33         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EK TCGA-IF-A4AK 
        0.07         0.07         4.14         0.10         1.38        31.76 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-MB-A5YA TCGA-MO-A47R 
      143.41        73.28         3.91        71.70         0.49         0.10 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-SG-A849 
       75.52        37.55        18.08        18.08       175.04         6.58 
TCGA-WK-A8XY TCGA-X6-A8C5 TCGA-X9-A971 
       65.46        32.75        12.36 

$subtype5
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A6BA 
       39.35        34.88        64.18        19.30        24.26        66.05 
TCGA-DX-A6YQ TCGA-FX-A3TO TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A6BZ 
        3.06        20.32        12.62        23.97        80.48         7.13 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-AA9N TCGA-UE-A6QU TCGA-WK-A8XS 
       11.70         6.35        81.01         7.76         0.72        72.72 
TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C6 
       17.26         8.52         8.35        24.62 

$subtype6
TCGA-DX-A1L2 TCGA-DX-A3U7 TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YU 
       59.24        42.77        26.47         2.07        66.31        23.54 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IS-A3K6 TCGA-IS-A3KA 
       33.07        35.67        41.33         9.80        28.21        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-SI-AA8B TCGA-WK-A8Y0 
        5.92        22.62         6.28         1.05         5.06        22.62 
TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C2 
       50.89        18.08        15.65 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.15     0.72     0.46     0.07     0.72     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   93.40   116.88   108.13   175.04    81.01    66.31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  17.210   24.095   14.550   14.960   19.810   22.620 
[1] "1.1 - 93.4 (17.2)"  "0.7 - 116.9 (24.1)" "0.5 - 108.1 (14.6)"
[4] "0.1 - 175.0 (15.0)" "0.7 - 81.0 (19.8)"  "1.1 - 66.3 (22.6)" 
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 16 18
  subtype3 10 17
  subtype4 22 11
  subtype5 17  5
  subtype6 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   16   18
  subtype3   10   17
  subtype4   22   11
  subtype5   17    5
  subtype6   14    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        8       16       10       22       17       14
  MALE         10       18       17       11        5        7
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    14
  subtype2     1                         2    22
  subtype3     0                         0    18
  subtype4     1                         3    28
  subtype5     2                         1    17
  subtype6     1                         2    15
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        0        1        2
  BLACK OR AFRICAN AMERICAN        2        2        0        3        1
  WHITE                           14       22       18       28       17
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           15
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 16  8
  subtype2 16  9
  subtype3 28 14
  subtype4  9  9
  subtype5 12  3
  subtype6 16  6
  subtype7  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      24       25       42       18       15       22        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       8        9       14        9        3        6        1 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y 
        2.04        38.24        36.69        18.54        59.24         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A48N 
        9.70       108.13        17.10        20.05        15.06        12.26 
TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BX TCGA-HB-A3YV 
        2.07        21.63        66.31        23.54        19.43         4.57 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-X6-A8C6 
        3.22         7.13        37.12         7.76        46.82        24.62 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A2J1 
       14.04        46.68        31.56        42.54         5.26        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BE 
       54.77         9.04        70.49        17.75         4.54        28.96 
TCGA-DX-A6BG TCGA-DX-A6BK TCGA-HB-A2OT TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-QQ-A5V2 
       17.79        16.18        26.89        36.39         2.37         1.84 
TCGA-QQ-A5VA TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        55.50         0.72         6.58        13.22         0.72 
TCGA-WK-A8XO 
       11.93 

$subtype3
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       42.77        14.99        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-HB-A5W3 
       25.08        12.49        66.05        23.44         0.10        12.62 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       23.97        80.48        21.37         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-K1-A3PN TCGA-K1-A42W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK 
       31.76        71.70        27.29         0.49         4.47        75.52 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       37.55        81.01        18.08        72.72        38.27        65.46 
TCGA-WK-A8XZ TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
       56.61        17.26        18.08         8.52        32.75        12.36 

$subtype4
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3UA TCGA-FX-A3RE TCGA-HS-A5N8 
       12.85        74.66         8.58        10.68         0.07         0.10 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R 
        5.92         3.91         5.26         5.69        15.65         0.10 
TCGA-PC-A5DN TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 
       38.63        10.52         3.88         4.80        41.49        10.82 

$subtype5
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A3UB TCGA-DX-A6B9 TCGA-FX-A48G TCGA-FX-A76Y 
       66.87        27.81        44.45        11.47         0.07         0.07 
TCGA-HS-A5NA TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
        9.80        28.21       116.88        73.28        22.62         6.28 
TCGA-MJ-A68J TCGA-QQ-A5VD TCGA-X2-A95T 
       11.08        21.01        50.89 

$subtype6
TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LT TCGA-DX-A48K TCGA-DX-A6YQ TCGA-DX-A7EF 
       76.41        60.30        23.08        19.30         3.06        21.30 
TCGA-FX-A3TO TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A9QH TCGA-N1-A6IA 
       20.32       143.41         1.05        11.70         3.88         4.08 
TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SI-AA8B 
        6.35         5.03        48.59        18.18        93.40         5.06 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       27.16        15.65         8.35         8.81 

$subtype7
TCGA-FX-A2QS TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IS-A3KA TCGA-QQ-A8VB 
        0.46         4.14        41.33        13.58       175.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    2.04     0.72     0.10     0.07     0.07     1.05     0.46 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  108.13    70.49    81.01    74.66   116.88   143.41   175.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  18.985   17.750   25.845    7.250   22.620   16.915   13.580 
[1] "2.0 - 108.1 (19.0)" "0.7 - 70.5 (17.8)"  "0.1 - 81.0 (25.8)" 
[4] "0.1 - 74.7 (7.2)"   "0.1 - 116.9 (22.6)" "1.1 - 143.4 (16.9)"
[7] "0.5 - 175.0 (13.6)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  8 17
  subtype2 11 14
  subtype3 25 17
  subtype4 14  4
  subtype5 12  3
  subtype6 12 10
  subtype7  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   17
  subtype2   11   14
  subtype3   25   17
  subtype4   14    4
  subtype5   12    3
  subtype6   12   10
  subtype7    5    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        8       11       25       14       12       12        5
  MALE         17       14       17        4        3       10        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    17
  subtype2     2                         1    15
  subtype3     0                         3    38
  subtype4     1                         0    13
  subtype5     1                         3     8
  subtype6     1                         2    16
  subtype7     0                         0     4
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        0        1        1
  BLACK OR AFRICAN AMERICAN        1        1        3        0        3
  WHITE                           17       15       38       13        8
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        0
  BLACK OR AFRICAN AMERICAN        2        0
  WHITE                           16        4
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 26 11
  subtype2 40 16
  subtype3 22 11
  subtype4 15 13
subtype1 subtype2 subtype3 subtype4 
      37       56       33       28 
subtype1 subtype2 subtype3 subtype4 
      11       16       11       13 
$subtype1
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        36.69        18.54        46.68        59.24        31.56 
TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A2J1 
        5.26        66.87         6.28        27.81         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       54.77        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YU 
       17.75        28.96         2.07        21.63        66.31        23.54 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-FX-A3TO TCGA-IE-A4EJ TCGA-IE-A6BZ 
       33.07        35.67        19.43        20.32         3.22         7.13 
TCGA-IF-A3RQ TCGA-LI-A9QH TCGA-MJ-A68J TCGA-QQ-A5V9 TCGA-UE-A6QT TCGA-UE-A6QU 
       37.12         3.88        11.08        46.82        13.22         0.72 
TCGA-X6-A8C6 
       24.62 

$subtype2
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       42.77        14.99        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       64.18         9.73        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ 
       72.72        12.49        11.47        66.05        23.44         0.10 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07         0.07         4.14        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
        9.80        80.48        21.37         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK 
        6.28        71.70        27.29         0.49         4.47        75.52 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX 
       37.55        81.01        18.08        21.01        72.72        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46        56.61        50.89        17.26        18.08         8.52 
TCGA-X6-A8C5 TCGA-X9-A971 
       32.75        12.36 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U8 
       14.04        42.54        76.41         9.04        23.08         4.54 
TCGA-DX-A48K TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-A8BO TCGA-HB-A2OT 
       19.30        17.79         3.06        21.30        26.33        26.89 
TCGA-IS-A3K7 TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DM 
      143.41        11.70         5.26         2.37         4.08         6.35 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF 
        5.03         1.84        18.08        48.59        18.18        93.40 
TCGA-QQ-A8VG TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC 
       55.50         6.58         5.06        11.93        22.62        27.16 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       15.65         8.35         8.81 

$subtype4
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A3UA 
        2.04        12.85        74.66        60.30         8.58        10.68 
TCGA-DX-A48N TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HS-A5N8 
       12.26         1.15         0.46         0.07         4.57         0.10 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A8JL TCGA-MJ-A850 
        5.92         1.05         3.91        36.39         5.69        15.65 
TCGA-MO-A47R TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-A68Q 
        0.10        38.63         7.76       175.04        10.52         0.72 
TCGA-SG-A6Z7 TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 
        3.88         4.80        41.49        10.82 

subtype1 subtype2 subtype3 subtype4 
    0.72     0.07     1.84     0.07 
subtype1 subtype2 subtype3 subtype4 
  108.13   116.88   143.41   175.04 
subtype1 subtype2 subtype3 subtype4 
   23.54    24.74    15.65     6.84 
[1] "0.7 - 108.1 (23.5)" "0.1 - 116.9 (24.7)" "1.8 - 143.4 (15.7)"
[4] "0.1 - 175.0 (6.8)" 
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 15 22
  subtype2 38 18
  subtype3 17 16
  subtype4 18 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   22
  subtype2   38   18
  subtype3   17   16
  subtype4   18   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       15       38       17       18
  MALE         22       18       16       11
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    21
  subtype2     1                         5    47
  subtype3     1                         2    26
  subtype4     1                         2    20
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        1        1
  BLACK OR AFRICAN AMERICAN        1        5        2        2
  WHITE                           21       47       26       20
[1] 3 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(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 15 11
  subtype2 10  1
  subtype3 26 13
  subtype4 14  6
  subtype5 18 12
  subtype6 16  3
  subtype7  4  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      26       11       39       20       30       19        9 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      11        1       13        6       12        3        5 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        38.24        18.54        46.68        59.24        31.56 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A3LU TCGA-DX-A3LY 
       66.87         6.28        27.81         9.70        70.49        17.10 
TCGA-DX-A3U5 TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BX 
       15.06         2.07        66.31        23.54        33.07        19.43 
TCGA-FX-A3TO TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-LI-A9QH TCGA-QQ-A5V9 
       20.32         3.22         7.13        37.12         3.88        46.82 
TCGA-UE-A6QU TCGA-X6-A8C6 
        0.72        24.62 

$subtype2
TCGA-DX-A1KZ TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3U6 
       36.69         5.26        59.47        54.77        23.08        17.75 
TCGA-DX-A6BE TCGA-DX-A8BO TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-UE-A6QT 
       28.96        26.33         2.37        11.08        13.22 

$subtype3
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       42.77        14.99        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 
       12.49        66.05        23.44         0.10        12.62        23.97 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN 
       80.48         8.94         1.38        25.22        31.76        71.70 
TCGA-K1-A42W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
       27.29         0.49         4.47        75.52        37.55        81.01 
TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X6-A7WA 
       18.08        72.72        38.27        65.46        56.61        17.26 
TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
        8.52        32.75        12.36 

$subtype4
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3M1 
       14.04        12.85        74.66         8.58       108.13        20.05 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BH TCGA-DX-A8BM TCGA-FX-A2QS TCGA-HB-A3YV 
       10.68        12.26        21.63        35.67         0.46         4.57 
TCGA-LI-A67I TCGA-MB-A8JL TCGA-MO-A47R TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A8VG 
        5.26         5.69         0.10        38.63         7.76        55.50 
TCGA-RN-A68Q TCGA-WK-A8XQ 
        0.72         4.80 

$subtype5
TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3U8 TCGA-DX-A48K 
       42.54        76.41        60.30         9.04         4.54        19.30 
TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-AATS TCGA-HB-A2OT TCGA-IS-A3K7 
       17.79         3.06        21.30         1.15        26.89       143.41 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5V2 
        1.05        11.70         4.08         6.35         5.03         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A849 TCGA-SI-AA8B 
       18.08        48.59        18.18        93.40         6.58         5.06 
TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       11.93        22.62        27.16        15.65         8.35         8.81 

$subtype6
TCGA-DX-A3UB TCGA-DX-A6B9 TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z 
       44.45        11.47         0.07         0.07         0.07         4.14 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
       41.33         9.80        21.37        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-QQ-A5VD TCGA-X2-A95T 
       73.28        22.62         6.28        36.39        21.01        50.89 
TCGA-X6-A7WB 
       18.08 

$subtype7
TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-MJ-A850 TCGA-QQ-A8VB TCGA-QQ-A8VH 
        0.10         5.92         3.91        15.65       175.04        10.52 
TCGA-SG-A6Z7 TCGA-WK-A8XT TCGA-X6-A8C7 
        3.88        41.49        10.82 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.72     2.37     0.10     0.10     1.05     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   70.49    59.47    81.01   108.13   143.41   116.88   175.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   21.93    23.08    27.22    11.47    13.79    21.01    10.52 
[1] "0.7 - 70.5 (21.9)"  "2.4 - 59.5 (23.1)"  "0.1 - 81.0 (27.2)" 
[4] "0.1 - 108.1 (11.5)" "1.1 - 143.4 (13.8)" "0.1 - 116.9 (21.0)"
[7] "0.1 - 175.0 (10.5)"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 11 15
  subtype2  5  6
  subtype3 23 16
  subtype4  9 12
  subtype5 16 14
  subtype6 16  3
  subtype7  8  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   15
  subtype2    5    6
  subtype3   23   16
  subtype4    9   12
  subtype5   16   14
  subtype6   16    3
  subtype7    8    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       11        5       23        9       16       16        8
  MALE         15        6       16       12       14        3        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    15
  subtype2     1                         1     5
  subtype3     0                         3    35
  subtype4     1                         1    16
  subtype5     1                         3    21
  subtype6     1                         2    14
  subtype7     0                         0     8
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        1        1
  BLACK OR AFRICAN AMERICAN        0        1        3        1        3
  WHITE                           15        5       35       16       21
                           clus
vv                          subtype6 subtype7
  ASIAN                            1        0
  BLACK OR AFRICAN AMERICAN        2        0
  WHITE                           14        8
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 41 25
  subtype2 14  7
  subtype3 47 20
subtype1 subtype2 subtype3 
      66       21       67 
subtype1 subtype2 subtype3 
      25        7       20 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        38.24        18.54        59.24        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE 
      108.13        20.05        17.75        19.30        12.26        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX 
       17.79        21.63        66.31        33.07        35.67        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ 
        1.15         0.46        20.32         4.57         7.13        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W 
      143.41         5.92         6.28         1.05         3.91        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        3.88         2.37         5.69        15.65         0.10         4.08 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB 
        6.35        38.63         5.03         7.76        46.82        48.59 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
      175.04        10.52         0.72         3.88         6.58         5.06 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-X6-A8C7 
       11.93         4.80        41.49        27.16        24.62        10.82 

$subtype2
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       36.69        46.68         6.28        70.49        17.10        15.06 
TCGA-DX-A3UA TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BO 
       10.68         2.07        16.18         3.06        23.54        26.33 
TCGA-HB-A2OT TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       26.89        11.08        18.08        21.01        93.40        55.50 
TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A8C2 
        0.72        22.62        15.65 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       14.04        12.85        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A7EF TCGA-FX-A3NJ TCGA-FX-A3RE 
       11.47        66.05        23.44        21.30         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07         4.14        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        31.76        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-MB-A5YA 
       22.62        71.70        36.39        27.29         5.26         0.49 
TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.47        75.52        37.55        81.01        18.08         1.84 
TCGA-QQ-A5VC TCGA-UE-A6QT TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       18.18        13.22        72.72        38.27        65.46        56.61 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 
       50.89        17.26        18.08         8.52         8.35        32.75 
TCGA-X9-A971 
       12.36 

subtype1 subtype2 subtype3 
    0.10     0.72     0.07 
subtype1 subtype2 subtype3 
  175.04    93.40   116.88 
subtype1 subtype2 subtype3 
   17.77    18.08    21.37 
[1] "0.1 - 175.0 (17.8)" "0.7 - 93.4 (18.1)"  "0.1 - 116.9 (21.4)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 32 35
  subtype2 11 10
  subtype3 44 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   35
  subtype2   11   10
  subtype3   44   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       11       44
  MALE         35       10       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    46
  subtype2     1                         2    14
  subtype3     3                         4    55
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        4        2        4
  WHITE                           46       14       55
[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"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 29 20
  subtype2 13  5
  subtype3 55 21
  subtype4  5  6
subtype1 subtype2 subtype3 subtype4 
      49       18       76       11 
subtype1 subtype2 subtype3 subtype4 
      20        5       21        6 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        38.24        18.54        59.24        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        23.08       108.13 
TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       20.05        10.68        12.26         2.07        17.79        21.63 
TCGA-DX-A6YS TCGA-DX-A8BL TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3TO 
       66.31        33.07        19.43         1.15         0.46        20.32 
TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-KF-A41W 
        4.57         7.13        37.12       143.41         5.92        11.70 
TCGA-LI-A9QH TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5V9 
        3.88         0.10         4.08         6.35         5.03        46.82 
TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-X6-A7WC 
       48.59        10.52         6.58         5.06        11.93        27.16 
TCGA-X6-A8C6 
       24.62 

$subtype2
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A6BE 
       36.69        46.68        70.49        17.75        19.30        28.96 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-A8BM TCGA-FX-A3RE TCGA-MB-A5Y9 
       16.18         3.06        21.30        35.67         0.07         2.37 
TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-UE-A6QU 
       11.08        18.08        93.40        55.50         0.72         0.72 

$subtype3
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 
       14.04        12.85         6.28        17.10        15.06        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       64.18         9.73        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6YU TCGA-DX-A8BO TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
       23.54        26.33         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         8.94         3.22         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       116.88        13.58        73.28        22.62         6.28 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H 
       71.70        36.39        27.29         5.26         0.49         4.47 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       75.52        37.55        81.01        18.08         7.76         1.84 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       18.18        21.01        13.22        72.72        38.27        65.46 
TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       56.61        22.62        50.89        17.26        18.08         8.52 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       15.65         8.35        32.75        12.36 

$subtype4
TCGA-DX-A2IZ TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A850 TCGA-PC-A5DN 
        8.58         1.05         3.91         5.69        15.65        38.63 
TCGA-QQ-A8VB TCGA-SG-A6Z7 TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 
      175.04         3.88         4.80        41.49        10.82 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.07     1.05 
subtype1 subtype2 subtype3 subtype4 
  143.41    93.40   116.88   175.04 
subtype1 subtype2 subtype3 subtype4 
   19.43    18.69    21.19     8.58 
[1] "0.1 - 143.4 (19.4)" "0.1 - 93.4 (18.7)"  "0.1 - 116.9 (21.2)"
[4] "1.1 - 175.0 (8.6)" 
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 22 28
  subtype2  9  9
  subtype3 48 28
  subtype4  8  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   28
  subtype2    9    9
  subtype3   48   28
  subtype4    8    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       22        9       48        8
  MALE         28        9       28        3
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    33
  subtype2     1                         1    13
  subtype3     3                         7    60
  subtype4     0                         1     9
D6V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        3        0
  BLACK OR AFRICAN AMERICAN        1        1        7        1
  WHITE                           33       13       60        9
[1] 3 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(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 27 22
  subtype2 30 14
  subtype3 16  4
subtype1 subtype2 subtype3 
      49       44       20 
subtype1 subtype2 subtype3 
      22       14        4 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V 
        2.04        38.24        18.54        74.66         5.26        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS 
       27.81        60.30         8.58         9.70        59.47         9.04 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF 
      108.13        20.05        19.30        12.26        28.96         2.07 
TCGA-DX-A6YS TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       66.31        19.43         1.15         0.46         0.07        20.32 
TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
        4.57        37.12       143.41         5.92         1.05         3.91 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DM 
       11.70         3.88         5.69        15.65         0.10         6.35 
TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 
       38.63         7.76        48.59       175.04        10.52         3.88 
TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7WC TCGA-X6-A8C6 
        5.06        11.93         4.80        41.49        27.16        24.62 
TCGA-X6-A8C7 
       10.82 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L 
       14.04        12.85        15.06        42.77        14.99        24.26 
TCGA-DX-A48O TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YU TCGA-FX-A3NJ TCGA-FX-A76Y 
       27.22        66.05        23.44        23.54         0.10         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 
       21.37         8.94        25.22        31.76        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA 
       22.62         6.28        71.70        36.39         5.26         0.49 
TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-WK-A8XS 
        4.47        75.52        81.01        18.08        21.01        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        56.61        50.89        17.26        18.08 
TCGA-X6-A8C5 TCGA-X9-A971 
       32.75        12.36 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A6YQ 
       36.69        17.10        17.75         4.54        10.68         3.06 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-MB-A5Y9 
       33.07        35.67        26.33        26.89         3.22         2.37 
TCGA-QC-A7B5 TCGA-QQ-A5VC TCGA-QQ-A8VG TCGA-SG-A849 TCGA-UE-A6QU TCGA-WK-A8Y0 
        5.03        18.18        55.50         6.58         0.72        22.62 
TCGA-X6-A8C2 TCGA-X6-A8C3 
       15.65         8.35 

subtype1 subtype2 subtype3 
    0.07     0.07     0.72 
subtype1 subtype2 subtype3 
  175.04    81.01    55.50 
subtype1 subtype2 subtype3 
  11.930   21.995   16.375 
[1] "0.1 - 175.0 (11.9)" "0.1 - 81.0 (22.0)"  "0.7 - 55.5 (16.4)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 28 22
  subtype2 30 14
  subtype3 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   22
  subtype2   30   14
  subtype3   10   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       28       30       10
  MALE         22       14       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    36
  subtype2     1                         3    36
  subtype3     2                         1    14
D7V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        2        3        1
  WHITE                           36       36       14
[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"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  8  2
  subtype2 10  9
  subtype3 19 11
  subtype4 10  4
  subtype5  7  1
  subtype6  7  5
  subtype7  6  2
  subtype8  6  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      10       19       30       14        8       12        8       12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        9       11        4        1        5        2        6 
$subtype1
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A8BL TCGA-DX-A8BM 
       36.69        17.10        10.68        28.96        33.07        35.67 
TCGA-FX-A3RE TCGA-LI-A9QH TCGA-QC-AA9N TCGA-WK-A8XQ 
        0.07         3.88         7.76         4.80 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Z 
        2.04        38.24        18.54        74.66        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A48N 
       60.30         9.70        59.47       108.13        20.05        12.26 
TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-HB-A3YV 
        2.07        66.31        19.43         1.15         0.46         4.57 
TCGA-IF-A3RQ 
       37.12 

$subtype3
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA TCGA-FX-A3NJ 
       42.77        14.99        24.26        27.22        66.05         0.10 
TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        0.07         4.14        23.97         9.80        80.48         8.94 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-K1-A3PN TCGA-MB-A5YA 
       25.22        31.76        13.58        73.28        71.70         0.49 
TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       75.52        81.01        18.08        72.72        38.27        65.46 
TCGA-WK-A8XZ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C5 TCGA-X9-A971 
       56.61        50.89        17.26        18.08        32.75        12.36 

$subtype4
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A6YU TCGA-DX-A8BO 
       14.04        12.85        15.06         4.54        23.54        26.33 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-LI-A67I TCGA-QQ-A5VC TCGA-WK-A8Y0 
       26.89         0.10         3.22         5.26        18.18        22.62 
TCGA-X6-A8C2 TCGA-X6-A8C3 
       15.65         8.35 

$subtype5
TCGA-DX-A6BB TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PO 
       23.44        12.62        21.37        22.62         6.28        36.39 
TCGA-MJ-A68H TCGA-QQ-A5VD 
        4.47        21.01 

$subtype6
TCGA-DX-A3LS TCGA-DX-A48K TCGA-FX-A3TO TCGA-IS-A3K7 TCGA-KF-A41W TCGA-PC-A5DM 
        9.04        19.30        20.32       143.41        11.70         6.35 
TCGA-PC-A5DN TCGA-QQ-A5VB TCGA-SI-AA8B TCGA-WK-A8XO TCGA-X6-A7WC TCGA-X6-A8C6 
       38.63        48.59         5.06        11.93        27.16        24.62 

$subtype7
TCGA-DX-A23T TCGA-DX-A3U6 TCGA-DX-A6YQ TCGA-MB-A5Y9 TCGA-QC-A7B5 TCGA-QQ-A8VG 
        5.26        17.75         3.06         2.37         5.03        55.50 
TCGA-SG-A849 TCGA-UE-A6QU 
        6.58         0.72 

$subtype8
TCGA-DX-A2IZ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A850 
        8.58         5.92         1.05         3.91         5.69        15.65 
TCGA-MO-A47R TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-WK-A8XT TCGA-X6-A8C7 
        0.10       175.04        10.52         3.88        41.49        10.82 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.07     0.46     0.07     0.10     4.47     5.06     0.72     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   36.69   108.13    81.01    26.89    36.39   143.41    55.50   175.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  13.890   20.050   26.220   14.550   21.190   19.810    5.145    7.250 
[1] "0.1 - 36.7 (13.9)"  "0.5 - 108.1 (20.1)" "0.1 - 81.0 (26.2)" 
[4] "0.1 - 26.9 (14.6)"  "4.5 - 36.4 (21.2)"  "5.1 - 143.4 (19.8)"
[7] "0.7 - 55.5 (5.1)"   "0.1 - 175.0 (7.2)" 
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1  4  6
  subtype2  7 13
  subtype3 22  8
  subtype4  9  5
  subtype5  5  3
  subtype6  7  5
  subtype7  4  4
  subtype8 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    7   13
  subtype3   22    8
  subtype4    9    5
  subtype5    5    3
  subtype6    7    5
  subtype7    4    4
  subtype8   10    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        4        7       22        9        5        7        4
  MALE          6       13        8        5        3        5        4
        clus
vv       subtype8
  FEMALE       10
  MALE          2
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1     8
  subtype2     0                         0    11
  subtype3     0                         1    27
  subtype4     1                         1     9
  subtype5     1                         2     5
  subtype6     0                         0    12
  subtype7     1                         0     5
  subtype8     1                         1     9
D8V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        1
  BLACK OR AFRICAN AMERICAN        1        0        1        1        2
  WHITE                            8       11       27        9        5
                           clus
vv                          subtype6 subtype7 subtype8
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                           12        5        9
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
