[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/10006228/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/10668110/SARC-TP.mergedcluster.txt"

nPatients in clinical file=114, in cluster file=242, common to both=114
[1]   8 114
[1] "CN_CNMF"
[1] 3
 1  2  3 
40 36 38 
 1  2  3 
40 36 38 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
19 21 33 13 13 11  4 
 1  2  3  4  5  6  7 
19 21 33 13 13 11  4 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
20 31 15 45 
 1  2  3  4 
20 31 15 45 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
30 22 16 30 13 
 1  2  3  4  5 
30 22 16 30 13 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
45 54 14 
 1  2  3 
45 54 14 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
35  9 16  6 47 
 1  2  3  4  5 
35  9 16  6 47 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
44 54 15 
 1  2  3 
44 54 15 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
42 54 17 
 1  2  3 
42 54 17 
[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 114 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          827           NA          745           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1291          960          908         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         1620         1309           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-A6B9 
         828          455          805         2212          763          349 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
        1669          328          496           63          224           51 
TCGA-DX-A6BK TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
          NA           14            3            2            2          818 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
          NA          126           NA          729            3         1257 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
         298           NA          650          272           98           42 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
         217           NA           NA          966           NA         4362 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
        3555           NA         2229           NA          688          191 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
          NA           NA         2181         1107          356          160 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
          72           15          173          136          337            3 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
         124         2297           NA           NA           NA           NA 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
          NA           56           NA           NA          553          639 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
          NA          402           22           NA          826          259 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=75,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=11,	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 114 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=48, 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 27 13
  subtype2 25 11
  subtype3 26 12
subtype1 subtype2 subtype3 
      40       36       38 
subtype1 subtype2 subtype3 
      13       11       12 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        29.85        74.66         5.26        66.87         6.28 
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        53.26         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       17.75        12.26        16.31         2.07         7.36         1.68 
TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IF-A3RQ TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-MB-A5Y9 
        0.46        26.89        37.12         5.92        22.62         2.37 
TCGA-MO-A47R TCGA-PC-A5DN TCGA-QQ-A5VA TCGA-SG-A6Z7 
        0.10        38.63        18.08         3.88 

$subtype2
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF 
       27.19        12.85        42.77        14.99        28.80        64.18 
TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV 
       26.47        54.87        10.78         0.07         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VE 
       21.37         8.94         3.22         7.13        13.58         6.28 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO 
        1.05        11.70         5.26         4.08         6.35        81.01 
TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-UE-A6QU TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       46.82        18.18         0.72        18.08        27.16         8.52 

$subtype3
TCGA-DX-A23U TCGA-DX-A2J4 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       76.41        43.04         4.54        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BK TCGA-FX-A3NJ TCGA-HS-A5N8 
       72.72        25.08        11.47        16.18         0.10         0.10 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38        25.22        31.76        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL 
       73.28         3.91        71.70        36.39         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5V2 
        4.47        11.08        75.52        37.55        18.08         1.84 
TCGA-QQ-A5VD TCGA-UE-A6QT 
       21.01        13.22 

subtype1 subtype2 subtype3 
    0.10     0.07     0.10 
subtype1 subtype2 subtype3 
  108.13    81.01   143.41 
subtype1 subtype2 subtype3 
  17.915   12.735   22.635 
[1] "0.1 - 108.1 (17.9)" "0.1 - 81.0 (12.7)"  "0.1 - 143.4 (22.6)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 16 24
  subtype2 25 11
  subtype3 21 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   24
  subtype2   25   11
  subtype3   21   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       16       25       21
  MALE         24       11       17
[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     2                         1    21
  subtype2     1                         3    27
  subtype3     1                         4    29
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        1        3        4
  WHITE                           21       27       29
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 13  6
  subtype2 15  6
  subtype3 22 11
  subtype4  7  6
  subtype5 10  3
  subtype6  8  3
  subtype7  3  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      19       21       33       13       13       11        4 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6        6       11        6        3        3        1 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y 
        2.04        27.19        24.49        18.54        42.44         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-HB-A3YV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        2.07         1.68         4.57         3.22         7.13        37.12 
TCGA-QQ-A5V9 
       46.82 

$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        29.85         5.26        53.26 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BE 
       43.04         9.04        70.49        17.75         4.54        16.31 
TCGA-DX-A6BG TCGA-DX-A6BK TCGA-HB-A2OT TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-QQ-A5V2 
        7.36        16.18        26.89        36.39         2.37         1.84 
TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-UE-A6QU 
       18.08        13.22         0.72 

$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-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 
       25.08        54.87        10.78         0.10        12.62        23.97 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        25.22        31.76 
TCGA-K1-A3PN TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
       71.70         0.49         4.47        75.52        37.55        81.01 
TCGA-PC-A5DP TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08        18.08         8.52 

$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-MO-A47R TCGA-PC-A5DN 
        5.92         3.91         5.26         5.69         0.10        38.63 
TCGA-SG-A6Z7 
        3.88 

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

$subtype6
TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LT TCGA-DX-A48K TCGA-IS-A3K7 TCGA-JV-A5VF 
       76.41        60.30        23.08        19.30       143.41         1.05 
TCGA-KF-A41W TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-X6-A7WC 
       11.70         4.08         6.35        18.18        27.16 

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

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1.68     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    41.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   15.06    16.31    25.08     5.69    22.62    19.30     8.86 
[1] "1.7 - 108.1 (15.1)" "0.7 - 70.5 (16.3)"  "0.1 - 81.0 (25.1)" 
[4] "0.1 - 74.7 (5.7)"   "0.1 - 116.9 (22.6)" "1.1 - 143.4 (19.3)"
[7] "0.5 - 41.3 (8.9)"  
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1  5 14
  subtype2  9 12
  subtype3 18 15
  subtype4 11  2
  subtype5 10  3
  subtype6  5  6
  subtype7  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   14
  subtype2    9   12
  subtype3   18   15
  subtype4   11    2
  subtype5   10    3
  subtype6    5    6
  subtype7    4    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        5        9       18       11       10        5        4
  MALE         14       12       15        2        3        6        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                         0    12
  subtype2     2                         1    11
  subtype3     0                         2    30
  subtype4     1                         0     8
  subtype5     1                         3     6
  subtype6     0                         2     7
  subtype7     0                         0     3
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        0        1        1
  BLACK OR AFRICAN AMERICAN        0        1        2        0        3
  WHITE                           12       11       30        8        6
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        2        0
  WHITE                            7        3
[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 13  7
  subtype2 23  8
  subtype3  8  7
  subtype4 32 13
subtype1 subtype2 subtype3 subtype4 
      20       31       15       45 
subtype1 subtype2 subtype3 subtype4 
       7        8        7       13 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3LT 
       14.04        29.85        76.41        60.30         9.04        23.08 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BG TCGA-HB-A2OT TCGA-IS-A3K7 
        4.54        10.68        19.30         7.36        26.89       143.41 
TCGA-KF-A41W TCGA-LI-A67I TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       11.70         5.26         4.08         6.35         1.84        18.08 
TCGA-QQ-A5VC TCGA-X6-A7WC 
       18.18        27.16 

$subtype2
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.54        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 
       31.56         5.26        66.87         6.28        27.81         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       53.26        43.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BH TCGA-IE-A4EJ 
       15.06        17.75        12.26        16.31         1.68         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-QQ-A5V9 TCGA-UE-A6QT 
        7.13        37.12         2.37        11.08        46.82        13.22 
TCGA-UE-A6QU 
        0.72 

$subtype3
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV 
       12.85        74.66         8.58         0.46         0.07         4.57 
TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A8JL 
        0.10         5.92         1.05         3.91        36.39         5.69 
TCGA-MO-A47R TCGA-PC-A5DN TCGA-SG-A6Z7 
        0.10        38.63         3.88 

$subtype4
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-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A48G 
       72.72        11.47        54.87        10.78         0.10         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37         8.94         1.38        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62         6.28        71.70 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
        0.49         4.47        75.52        37.55        81.01        18.08 
TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WD 
       21.01        18.08         8.52 

subtype1 subtype2 subtype3 subtype4 
    1.84     0.72     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  143.41   108.13    74.66   116.88 
subtype1 subtype2 subtype3 subtype4 
   16.06    17.75     4.57    23.97 
[1] "1.8 - 143.4 (16.1)" "0.7 - 108.1 (17.8)" "0.1 - 74.7 (4.6)"  
[4] "0.1 - 116.9 (24.0)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  9 11
  subtype2 11 20
  subtype3 11  4
  subtype4 29 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   11
  subtype2   11   20
  subtype3   11    4
  subtype4   29   16
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       11       11       29
  MALE         11       20        4       16
[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     0                         2    14
  subtype2     2                         1    14
  subtype3     1                         1     9
  subtype4     1                         4    37
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        2        1        1
  BLACK OR AFRICAN AMERICAN        2        1        1        4
  WHITE                           14       14        9       37
[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 20 10
  subtype2 14  8
  subtype3 12  4
  subtype4 20 10
  subtype5 10  3
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       22       16       30       13 
subtype1 subtype2 subtype3 subtype4 subtype5 
      10        8        4       10        3 
$subtype1
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        27.19        24.49        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.44        31.56         5.26        66.87         6.28        27.81 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        9.70        53.26        43.04        70.49        17.10        15.06 
TCGA-DX-A3U6 TCGA-DX-A6BE TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-LI-A67I 
       17.75        16.31         3.22         7.13        37.12         5.26 
TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-UE-A6QT TCGA-UE-A6QU 
        2.37        11.08        46.82        18.08        13.22         0.72 

$subtype2
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3UA 
       12.85        74.66         8.58       108.13        20.05        10.68 
TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A6B9 TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A3YV 
       44.45        12.26        11.47         1.68         0.46         4.57 
TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A8JL 
        0.10         5.92         1.05         3.91        36.39         5.69 
TCGA-MO-A47R TCGA-PC-A5DN TCGA-QQ-A5VD TCGA-SG-A6Z7 
        0.10        38.63        21.01         3.88 

$subtype3
TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U8 
       29.85        76.41        60.30         9.04        23.08         4.54 
TCGA-DX-A48K TCGA-DX-A6BG TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-KF-A41W TCGA-N1-A6IA 
       19.30         7.36        26.89       143.41        11.70         4.08 
TCGA-PC-A5DM TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-X6-A7WC 
        6.35         1.84        18.18        27.16 

$subtype4
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-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV 
       54.87        10.78         0.10        12.62        23.97        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN TCGA-MB-A5YA 
        8.94         1.38        25.22        31.76        71.70         0.49 
TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-X6-A7WD 
        4.47        75.52        37.55        81.01        18.08         8.52 

$subtype5
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        0.07         0.07         4.14        41.33         9.80        21.37 
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-X6-A7WB 
       18.08 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.72     0.10     1.84     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
   70.49   108.13   143.41    81.01   116.88 
subtype1 subtype2 subtype3 subtype4 subtype5 
  17.425    9.630   18.740   25.845   18.080 
[1] "0.7 - 70.5 (17.4)"  "0.1 - 108.1 (9.6)"  "1.8 - 143.4 (18.7)"
[4] "0.1 - 81.0 (25.8)"  "0.1 - 116.9 (18.1)"
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 13 17
  subtype2 12 10
  subtype3  6 10
  subtype4 16 14
  subtype5 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   17
  subtype2   12   10
  subtype3    6   10
  subtype4   16   14
  subtype5   13    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       13       12        6       16       13
  MALE         17       10       10       14        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    13
  subtype2     1                         2    15
  subtype3     0                         2    10
  subtype4     0                         2    27
  subtype5     1                         1     9
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        0        0        1
  BLACK OR AFRICAN AMERICAN        1        2        2        2        1
  WHITE                           13       15       10       27        9
[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"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 29 16
  subtype2 38 16
  subtype3 10  4
subtype1 subtype2 subtype3 
      45       54       14 
subtype1 subtype2 subtype3 
      16       16        4 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.54        42.44        31.56        29.85 
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        53.26        43.04         9.04        23.08 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BG 
      108.13        20.05        17.75        19.30        12.26         7.36 
TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        1.68         0.46         4.57         7.13        37.12       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W TCGA-MB-A5Y9 
        5.92         6.28         1.05         3.91        11.70         2.37 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 
        5.69         0.10         4.08         6.35        38.63        46.82 
TCGA-QQ-A5VD TCGA-SG-A6Z7 TCGA-X6-A7WC 
       21.01         3.88        27.16 

$subtype2
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-A6B9 
       27.22        14.96        26.47        72.72        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z 
       54.87        10.78         0.10         0.07         0.07         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO 
      116.88        13.58        73.28        22.62        71.70        36.39 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
        5.26         0.49         4.47        75.52        37.55        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       18.08         1.84        18.18        13.22        18.08         8.52 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       24.49        46.68         6.28        70.49        17.10        15.06 
TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BK TCGA-HB-A2OT TCGA-MJ-A68J 
       10.68        16.31         2.07        16.18        26.89        11.08 
TCGA-QQ-A5VA TCGA-UE-A6QU 
       18.08         0.72 

subtype1 subtype2 subtype3 
    0.10     0.07     0.72 
subtype1 subtype2 subtype3 
  143.41   116.88    70.49 
subtype1 subtype2 subtype3 
  17.750   18.130   16.245 
[1] "0.1 - 143.4 (17.8)" "0.1 - 116.9 (18.1)" "0.7 - 70.5 (16.2)" 
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 21 24
  subtype2 33 21
  subtype3  7  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   24
  subtype2   33   21
  subtype3    7    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       33        7
  MALE         24       21        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    25
  subtype2     2                         3    44
  subtype3     1                         2     8
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        1
  BLACK OR AFRICAN AMERICAN        3        3        2
  WHITE                           25       44        8
[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 23 12
  subtype2  6  3
  subtype3 12  4
  subtype4  2  4
  subtype5 34 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      35        9       16        6       47 
subtype1 subtype2 subtype3 subtype4 subtype5 
      12        3        4        4       13 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.54        42.44        31.56        29.85 
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        53.26        43.04         9.04        23.08       108.13 
TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS 
       20.05        12.26         2.07         7.36         1.68         0.46 
TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-KF-A41W TCGA-MO-A47R 
        4.57         7.13        37.12       143.41        11.70         0.10 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 TCGA-X6-A7WC 
        4.08         6.35        38.63        46.82        27.16 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-HS-A5N8 TCGA-IE-A4EJ 
       14.04        12.85        15.06         4.54         0.10         3.22 
TCGA-LI-A67I TCGA-QQ-A5V2 TCGA-UE-A6QT 
        5.26         1.84        13.22 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 
       24.49        46.68         6.28        70.49        17.10        17.75 
TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BK TCGA-HB-A2OT TCGA-MB-A5Y9 
       10.68        19.30        16.31        16.18        26.89         2.37 
TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-UE-A6QU 
       11.08        18.08        18.18         0.72 

$subtype4
TCGA-DX-A2IZ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL TCGA-SG-A6Z7 
        8.58         5.92         1.05         3.91         5.69         3.88 

$subtype5
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-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ 
       72.72        25.08        11.47        54.87        10.78         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        0.07         0.07         4.14        12.62        23.97         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         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-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL 
       71.70        36.39         0.49         4.47        75.52        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-X6-A7WB TCGA-X6-A7WD 
       81.01        18.08        21.01        18.08         8.52 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.10     0.72     1.05     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  143.41    15.06    70.49     8.58   116.88 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.080    5.260   17.425    4.800   23.970 
[1] "0.1 - 143.4 (23.1)" "0.1 - 15.1 (5.3)"   "0.7 - 70.5 (17.4)" 
[4] "1.1 - 8.6 (4.8)"    "0.1 - 116.9 (24.0)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 15 20
  subtype2  4  5
  subtype3  8  8
  subtype4  5  1
  subtype5 29 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   20
  subtype2    4    5
  subtype3    8    8
  subtype4    5    1
  subtype5   29   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       15        4        8        5       29
  MALE         20        5        8        1       18
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    18
  subtype2     1                         0     5
  subtype3     1                         2    10
  subtype4     0                         1     4
  subtype5     1                         4    40
D6V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        1        0        1
  BLACK OR AFRICAN AMERICAN        1        0        2        1        4
  WHITE                           18        5       10        4       40
[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"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 28 16
  subtype2 39 15
  subtype3 10  5
subtype1 subtype2 subtype3 
      44       54       15 
subtype1 subtype2 subtype3 
      16       15        5 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.54        42.44        31.56        29.85 
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        53.26        43.04         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        16.31 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IE-A6BZ 
        2.07         7.36         1.68         0.46         4.57         7.13 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W 
       37.12       143.41         5.92         1.05         3.91        11.70 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 
        5.69         0.10         4.08         6.35        38.63        46.82 
TCGA-SG-A6Z7 TCGA-X6-A7WC 
        3.88        27.16 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       14.04        12.85        42.77        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       28.80        34.88        64.18         9.73        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        25.08        11.47        54.87 
TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 
       10.78         0.10         0.07         0.07         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97         0.10         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        31.76        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I 
       73.28        22.62         6.28        71.70        36.39         5.26 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
        0.49         4.47        75.52        37.55        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
        1.84        18.18        21.01        13.22        18.08         8.52 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       24.49        46.68         6.28        70.49        17.10        15.06 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A6BK TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-MB-A5Y9 
        4.54        10.68        16.18        26.89         3.22         2.37 
TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-UE-A6QU 
       11.08        18.08         0.72 

subtype1 subtype2 subtype3 
    0.10     0.07     0.72 
subtype1 subtype2 subtype3 
  143.41   116.88    70.49 
subtype1 subtype2 subtype3 
  17.030   19.595   15.060 
[1] "0.1 - 143.4 (17.0)" "0.1 - 116.9 (19.6)" "0.7 - 70.5 (15.1)" 
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 21 23
  subtype2 33 21
  subtype3  7  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   23
  subtype2   33   21
  subtype3    7    8
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       33        7
  MALE         23       21        8
[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    25
  subtype2     2                         4    44
  subtype3     1                         2     8
D7V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        1
  BLACK OR AFRICAN AMERICAN        2        4        2
  WHITE                           25       44        8
[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 26 16
  subtype2 38 16
  subtype3 13  4
subtype1 subtype2 subtype3 
      42       54       17 
subtype1 subtype2 subtype3 
      16       16        4 
$subtype1
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
        2.04        27.19        18.54        42.44        31.56        29.85 
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        53.26        43.04         9.04        23.08 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
      108.13        20.05        12.26         2.07         7.36         1.68 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        0.46         0.07         4.57         7.13        37.12       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-KF-A41W TCGA-MB-A8JL TCGA-MO-A47R 
        5.92         1.05         3.91        11.70         5.69         0.10 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 TCGA-SG-A6Z7 TCGA-X6-A7WC 
        4.08         6.35        38.63        46.82         3.88        27.16 

$subtype2
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       14.04        12.85        15.06        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A43Z 
       11.47        54.87        10.78         0.10         0.07         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62         6.28        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL 
       36.39         5.26         0.49         4.47        75.52        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-UE-A6QT TCGA-X6-A7WB TCGA-X6-A7WD 
       81.01        18.08         1.84        13.22        18.08         8.52 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 
       24.49        46.68         6.28        70.49        17.10        17.75 
TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BK TCGA-HB-A2OT TCGA-MB-A5Y9 
       10.68        19.30        16.31        16.18        26.89         2.37 
TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QU 
       11.08        18.08        18.18        21.01         0.72 

subtype1 subtype2 subtype3 
    0.07     0.07     0.72 
subtype1 subtype2 subtype3 
  143.41   116.88    70.49 
subtype1 subtype2 subtype3 
   11.98    18.08    17.75 
[1] "0.1 - 143.4 (12.0)" "0.1 - 116.9 (18.1)" "0.7 - 70.5 (17.8)" 
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 21 21
  subtype2 32 22
  subtype3  8  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   21
  subtype2   32   22
  subtype3    8    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       32        8
  MALE         21       22        9
[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    23
  subtype2     2                         4    43
  subtype3     1                         2    11
D8V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        1
  BLACK OR AFRICAN AMERICAN        2        4        2
  WHITE                           23       43       11
[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"
