[1] "ofn"        "-oTPCPG-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/PCPG-TP/15087180/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.mergedcluster.txt"

nPatients in clinical file=179, in cluster file=179, common to both=179
[1]  10 179
[1] "CN_CNMF"
[1] 3
 1  2  3 
60 63 39 
 1  2  3 
60 63 39 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
45 85 49 
 1  2  3 
45 85 49 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6 
14  9 20  6 17 13 
 1  2  3  4  5  6 
14  9 20  6 17 13 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
33 18 28 
 1  2  3 
33 18 28 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
39 69 50 21 
 1  2  3  4 
39 69 50 21 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
39 71 48 21 
 1  2  3  4 
39 71 48 21 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
75 65 39 
 1  2  3 
75 65 39 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
77 59 18 25 
 1  2  3  4 
77 59 18 25 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5 
36 64 12 42 24 
 1  2  3  4  5 
36 64 12 42 24 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
80 61 18 19 
 1  2  3  4 
80 61 18 19 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 179 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=163,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 179 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 57  3
  subtype2 62  1
  subtype3 37  2
subtype1 subtype2 subtype3 
      60       63       39 
subtype1 subtype2 subtype3 
       3        1        2 
$subtype1
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GO 
       31.46         2.27        17.95        81.70        28.08        35.01 
TCGA-QR-A6H1 TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70P TCGA-QR-A70W TCGA-QT-A5XK 
       14.17         6.31        26.83       117.14        41.79         6.94 
TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RW-A67V TCGA-RW-A67W 
        0.72         2.30         4.41       108.26        86.89        19.86 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WM 
       13.32         1.22         7.96         1.78        20.09        30.21 
TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF 
       37.25        40.70        25.32        18.08       114.77        82.62 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MQ 
       67.50       110.04        15.52       111.25         1.41        68.61 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
        3.12        24.66        19.92        14.20         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-WB-A80K TCGA-WB-A80O 
       12.03        12.49        16.60        17.69        34.82         4.21 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F 
      316.73        29.16        19.59        33.90        35.84        57.11 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W 
       38.76        42.54        53.69         1.61        18.28        78.21 

$subtype2
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GU TCGA-QR-A6GY TCGA-QR-A6GZ 
       29.03        17.75         5.88        58.88         1.05        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A706 
        9.21         9.93        14.27        31.53        15.58         4.11 
TCGA-QR-A70C TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70X TCGA-QR-A7IN TCGA-QR-A7IP 
      116.19         2.33        29.92         6.02        12.39        17.95 
TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC 
        1.81         0.79        13.08        77.98         0.92         8.09 
TCGA-RW-A684 TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A8AZ 
        1.05        72.79        15.02        41.88         4.41         2.89 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       35.51        31.04        37.58        30.51        27.91        20.58 
TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QD TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
       12.66         9.73       109.25        81.93       106.75       110.53 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HH TCGA-WB-A80L 
       49.61        25.15        13.32        25.32        25.61        34.26 
TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81A 
        4.47       127.56        32.88        41.23        32.61        24.16 
TCGA-WB-A81E TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81V 
       37.18        22.32        24.36        40.04        45.83        71.05 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       93.11       103.17        20.19 

$subtype3
TCGA-QR-A6GR TCGA-QR-A6GS TCGA-QR-A6GT TCGA-QR-A6GX TCGA-QR-A700 TCGA-QR-A702 
       23.11         1.25       137.59        19.04        32.15         1.28 
TCGA-QR-A70D TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70R TCGA-QT-A5XJ 
        0.23        13.12         9.01         1.41        14.20        36.23 
TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
       25.18        50.63         2.93         7.10        33.30        23.80 
TCGA-RW-A685 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WL TCGA-S7-A7WQ 
        0.85        11.70        13.05         6.28        31.59        26.96 
TCGA-S7-A7X1 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-TT-A6YJ 
       18.94         0.10        51.22       121.05        19.76         4.34 
TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A81P 
       17.16        10.65         4.73         5.98        34.03        12.99 
TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A820 
       24.82        23.77        10.16 

subtype1 subtype2 subtype3 
    0.72     0.79     0.10 
subtype1 subtype2 subtype3 
  316.73   127.56   137.59 
subtype1 subtype2 subtype3 
  22.375   25.320   14.200 
[1] "0.7 - 316.7 (22.4)" "0.8 - 127.6 (25.3)" "0.1 - 137.6 (14.2)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 33 27
  subtype2 33 30
  subtype3 22 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   27
  subtype2   33   30
  subtype3   22   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       33       22
  MALE         27       30       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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         4
  subtype2                                0     2                        10
  subtype3                                0     0                         5
          vv
clus       WHITE
  subtype1    51
  subtype2    50
  subtype3    33
D1V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   3        2        0
  BLACK OR AFRICAN AMERICAN               4       10        5
  WHITE                                  51       50       33
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1  0 51
  subtype2  2 51
  subtype3  0 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   51
  subtype2    2   51
  subtype3    0   26
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        0
  NOT HISPANIC OR LATINO       51       51       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 42  3
  subtype2 82  3
  subtype3 49  0
subtype1 subtype2 subtype3 
      45       85       49 
subtype1 subtype2 subtype3 
       3        3        0 
$subtype1
TCGA-P7-A5NX TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GZ 
       26.89        17.75         5.88       137.59        58.88        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H6 TCGA-QR-A700 TCGA-QR-A705 TCGA-QR-A70A 
        9.21        14.27        15.58        32.15        10.42        69.67 
TCGA-QR-A70D TCGA-QR-A70G TCGA-QR-A70I TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A70T 
        0.23         2.33        29.92       117.14         4.60         8.78 
TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RM-A68T 
       12.39        17.95        36.23         1.81        13.08        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A68D TCGA-RW-A68F 
        0.92       108.26        33.30        23.80        72.79        15.02 
TCGA-RW-A7CZ TCGA-S7-A7WP TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SR-A6MT TCGA-SR-A6MX 
        4.41        31.04       109.25        67.50       106.75         3.12 
TCGA-SR-A6N0 TCGA-W2-A7H7 TCGA-WB-A80P TCGA-WB-A81E TCGA-WB-A81G TCGA-WB-A81I 
       49.61        17.16       316.73        37.18        38.76        22.32 
TCGA-WB-A81Q TCGA-WB-A822 TCGA-XG-A823 
       24.82       103.17        20.19 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GR 
       31.46         2.27        17.95        81.70        35.01        23.11 
TCGA-QR-A6GS TCGA-QR-A6GW TCGA-QR-A6GY TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H4 
        1.25        16.14         1.05        14.17         9.93        87.48 
TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70E TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70M 
        1.28        13.08         6.31        26.83         9.01        33.99 
TCGA-QR-A70O TCGA-QR-A70R TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK 
        3.65        14.20        48.43         0.07        41.79         6.94 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RT-A6YC 
       25.18         2.30         4.41         0.79        50.63         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
       86.89        19.86         7.10         0.85         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68G TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       13.05         7.96        41.88         2.89        20.09        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WX 
       30.21        37.25        40.70        37.58        30.51        25.32 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 
       18.08       114.77        82.62       110.04        15.52         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN 
        0.10        51.22        81.93        24.66         4.34        19.92 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-WB-A80M 
        1.18        19.86        12.03        12.49        17.69         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 
        4.73         4.21       127.56        29.16        19.59         5.98 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81M 
       34.03        33.90        35.84        57.11        24.36        45.83 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        23.77        18.28        71.05        78.21 
TCGA-WB-A820 
       10.16 

$subtype3
TCGA-P8-A5KC TCGA-PR-A5PH TCGA-QR-A6GX TCGA-QR-A6H5 TCGA-QR-A6ZZ TCGA-QR-A703 
       29.03        28.08        19.04        31.53         1.58        38.37 
TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70C TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70X 
        4.11         1.15       116.19        13.12         1.41         6.02 
TCGA-QT-A5XM TCGA-RW-A67X TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A7D0 
        0.72         2.93         1.05        13.32         6.28         1.78 
TCGA-S7-A7WO TCGA-S7-A7WQ TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       35.51        26.96        27.91        20.58        12.66        18.94 
TCGA-SA-A6C2 TCGA-SP-A6QH TCGA-SP-A6QK TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MU 
        9.73        72.43       111.25        68.61        79.20       110.53 
TCGA-SR-A6MV TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
      121.05        19.76        25.15        13.32        25.32        14.20 
TCGA-W2-A7HE TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A814 
       16.60        25.61        10.65        34.82        34.26        32.88 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81A TCGA-WB-A81H TCGA-WB-A81K TCGA-WB-A81N 
       41.23        32.61        24.16        42.54        40.04        53.69 
TCGA-WB-A821 
       93.11 

subtype1 subtype2 subtype3 
    0.23     0.07     0.72 
subtype1 subtype2 subtype3 
  316.73   127.56   121.05 
subtype1 subtype2 subtype3 
   24.82    18.28    25.32 
[1] "0.2 - 316.7 (24.8)" "0.1 - 127.6 (18.3)" "0.7 - 121.0 (25.3)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 21 24
  subtype2 48 37
  subtype3 32 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   24
  subtype2   48   37
  subtype3   32   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       21       48       32
  MALE         24       37       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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         7
  subtype2                                1     2                         5
  subtype3                                0     3                         8
          vv
clus       WHITE
  subtype1    36
  subtype2    74
  subtype3    38
D2V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                   1        2        3
  BLACK OR AFRICAN AMERICAN               7        5        8
  WHITE                                  36       74       38
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1  2 34
  subtype2  2 63
  subtype3  1 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   34
  subtype2    2   63
  subtype3    1   41
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        1
  NOT HISPANIC OR LATINO       34       63       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 14  0
  subtype2  8  1
  subtype3 20  0
  subtype4  6  0
  subtype5 16  1
  subtype6 13  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      14        9       20        6       17       13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       0        1        0        0        1        0 
$subtype1
TCGA-P7-A5NX TCGA-QR-A70W TCGA-QT-A69Q TCGA-RW-A685 TCGA-RW-A68B TCGA-RW-A68D 
       26.89        41.79         0.79         0.85         7.96        72.79 
TCGA-RW-A68G TCGA-S7-A7WU TCGA-SR-A6MQ TCGA-SR-A6MZ TCGA-TT-A6YN TCGA-W2-A7HC 
       41.88        30.51        68.61        19.76        19.92        12.03 
TCGA-WB-A81P TCGA-WB-A81W 
       12.99        78.21 

$subtype2
TCGA-P8-A5KC TCGA-QR-A6GT TCGA-RM-A68W TCGA-RW-A680 TCGA-S7-A7WX TCGA-SR-A6MX 
       29.03       137.59         0.92        33.30        25.32         3.12 
TCGA-SR-A6MY TCGA-WB-A818 TCGA-WB-A81T 
       24.66        34.03        18.28 

$subtype3
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN 
        2.27        81.70        35.01         6.94         0.72        25.18 
TCGA-QT-A5XO TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A688 TCGA-RW-A689 TCGA-S7-A7WL 
        2.30        50.63         8.09         1.22        11.70        31.59 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7X2 TCGA-SP-A6QJ TCGA-W2-A7HF 
       30.21        37.25        40.70        18.08        15.52        17.69 
TCGA-WB-A819 TCGA-WB-A81V 
       33.90        71.05 

$subtype4
TCGA-P8-A6RX TCGA-QT-A5XP TCGA-RW-A67X TCGA-RW-A68A TCGA-S7-A7WV TCGA-SP-A6QH 
       17.75         4.41         2.93        13.05        27.91        72.43 

$subtype5
TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GU TCGA-QR-A6H2 TCGA-QT-A5XJ 
        5.88        17.95        28.08        58.88         9.93        36.23 
TCGA-RM-A68T TCGA-RT-A6Y9 TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A68F TCGA-RW-A8AZ 
       77.98       108.26        86.89        23.80        15.02         2.89 
TCGA-S7-A7WW TCGA-SA-A6C2 TCGA-WB-A817 TCGA-WB-A81G TCGA-WB-A81M 
       20.58         9.73        32.61        38.76        45.83 

$subtype6
TCGA-QR-A6GZ TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RW-A68C TCGA-RX-A8JQ TCGA-S7-A7WP 
       30.51         1.81        13.08         6.28        20.09        31.04 
TCGA-S7-A7WQ TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A815 
       26.96        12.66        18.94       127.56        32.88         5.98 
TCGA-WB-A81S 
       23.77 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.79     0.92     0.72     2.93     2.89     1.81 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   78.21   137.59    81.70    72.43   108.26   127.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.405   25.320   21.630   15.400   28.080   20.090 
[1] "0.8 - 78.2 (23.4)"  "0.9 - 137.6 (25.3)" "0.7 - 81.7 (21.6)" 
[4] "2.9 - 72.4 (15.4)"  "2.9 - 108.3 (28.1)" "1.8 - 127.6 (20.1)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1  8  6
  subtype2  4  5
  subtype3 11  9
  subtype4  4  2
  subtype5  7 10
  subtype6  6  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    6
  subtype2    4    5
  subtype3   11    9
  subtype4    4    2
  subtype5    7   10
  subtype6    6    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        8        4       11        4        7        6
  MALE          6        5        9        2       10        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     2                         0    11
  subtype2     0                         0     9
  subtype3     0                         4    16
  subtype4     1                         1     4
  subtype5     1                         3    13
  subtype6     0                         1    12
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        0        0        1        1
  BLACK OR AFRICAN AMERICAN        0        0        4        1        3
  WHITE                           11        9       16        4       13
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        1
  WHITE                           12
[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"
D3V5, binary
          cls
clus        0  1
  subtype1  1  9
  subtype2  0  7
  subtype3  0 16
  subtype4  0  4
  subtype5  0 11
  subtype6  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    9
  subtype2    0    7
  subtype3    0   16
  subtype4    0    4
  subtype5    0   11
  subtype6    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        0        0        0        0
  NOT HISPANIC OR LATINO        9        7       16        4       11       11
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 31  2
  subtype2 18  0
  subtype3 28  0
subtype1 subtype2 subtype3 
      33       18       28 
subtype1 subtype2 subtype3 
       2        0        0 
$subtype1
TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GT 
       26.89        29.03         5.88        17.95        28.08       137.59 
TCGA-QR-A6GU TCGA-QT-A5XJ TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67V 
       58.88        36.23        77.98         0.92       108.26        86.89 
TCGA-RW-A680 TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A8AZ TCGA-S7-A7WU 
       33.30         6.28        15.02        41.88         2.89        30.51 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-SA-A6C2 TCGA-SP-A6QH TCGA-SR-A6MX 
       20.58        25.32        12.66         9.73        72.43         3.12 
TCGA-SR-A6MY TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A817 TCGA-WB-A81G 
       24.66       127.56        32.88         5.98        32.61        38.76 
TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S 
       45.83        12.99        23.77 

$subtype2
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GZ TCGA-QR-A70W TCGA-QT-A5XK TCGA-RW-A685 
        2.27        81.70        30.51        41.79         6.94         0.85 
TCGA-RW-A688 TCGA-RX-A8JQ TCGA-S7-A7WR TCGA-S7-A7X2 TCGA-SR-A6MQ TCGA-SR-A6MZ 
        1.22        20.09        40.70        18.08        68.61        19.76 
TCGA-TT-A6YN TCGA-W2-A7HC TCGA-WB-A818 TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       19.92        12.03        34.03        18.28        71.05        78.21 

$subtype3
TCGA-P8-A6RX TCGA-QR-A6GO TCGA-QR-A6H2 TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       17.75        35.01         9.93         1.81         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RT-A6YA TCGA-RT-A6YC 
        2.30         4.41         0.79        13.08        50.63         8.09 
TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
        2.93        23.80        11.70        13.05         7.96        72.79 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WV 
       31.59        30.21        37.25        31.04        26.96        27.91 
TCGA-S7-A7X1 TCGA-SP-A6QJ TCGA-W2-A7HF TCGA-WB-A819 
       18.94        15.52        17.69        33.90 

subtype1 subtype2 subtype3 
    0.92     0.85     0.72 
subtype1 subtype2 subtype3 
  137.59    81.70    72.79 
subtype1 subtype2 subtype3 
  28.080   20.005   17.720 
[1] "0.9 - 137.6 (28.1)" "0.8 - 81.7 (20.0)"  "0.7 - 72.8 (17.7)" 
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1 20 13
  subtype2 10  8
  subtype3 10 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   13
  subtype2   10    8
  subtype3   10   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       10       10
  MALE         13        8       18
[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    28
  subtype2     1                         1    16
  subtype3     2                         4    21
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        4        1        4
  WHITE                           28       16       21
[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"
D4V5, binary
          cls
clus        0  1
  subtype1  1 24
  subtype2  0 15
  subtype3  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   24
  subtype2    0   15
  subtype3    0   19
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       24       15       19
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 37  2
  subtype2 67  2
  subtype3 48  2
  subtype4 21  0
subtype1 subtype2 subtype3 subtype4 
      39       69       50       21 
subtype1 subtype2 subtype3 subtype4 
       2        2        2        0 
$subtype1
TCGA-P7-A5NX TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H6 
       26.89        58.88        19.04         9.21        14.27        15.58 
TCGA-QR-A705 TCGA-QR-A707 TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70P 
       10.42        13.08         0.23         6.31        29.92       117.14 
TCGA-QR-A70Q TCGA-QR-A70T TCGA-QR-A70V TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-RM-A68T 
        4.60         8.78         0.07        17.95        36.23        77.98 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A688 
        0.92       108.26         7.10        33.30        23.80         1.22 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WU TCGA-SP-A6QD TCGA-SP-A6QG 
       72.79        15.02         4.41        30.51       109.25        67.50 
TCGA-SR-A6MT TCGA-SR-A6MX TCGA-TT-A6YJ TCGA-W2-A7H7 TCGA-W2-A7HF TCGA-W2-A7HH 
      106.75         3.12         4.34        17.16        17.69        25.61 
TCGA-WB-A80P TCGA-WB-A81E TCGA-WB-A81G 
      316.73        37.18        38.76 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GW 
       31.46         2.27        81.70        35.01         1.25        16.14 
TCGA-QR-A6H1 TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70K TCGA-QR-A70M 
       14.17        87.48         1.28        26.83         9.01        33.99 
TCGA-QR-A70O TCGA-QR-A70U TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN 
        3.65        48.43        41.79         6.94         0.72        25.18 
TCGA-QT-A5XP TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A684 TCGA-RW-A689 
        4.41        50.63         8.09        19.86         1.05        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
       13.05         7.96         1.78        20.09        31.59        30.21 
TCGA-S7-A7WN TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC 
       37.25        40.70        37.58        25.32        18.08       114.77 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       82.62       110.04        15.52         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
       68.61        24.66        19.92        14.20         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V 
       12.03        12.49         4.47         4.73         4.21        29.16 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81M 
       34.03        33.90        35.84        57.11        24.36        45.83 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       53.69        12.99        24.82         1.61        23.77        18.28 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       71.05        78.21        10.16 

$subtype3
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GT 
       29.03        17.75         5.88        17.95        28.08       137.59 
TCGA-QR-A6GY TCGA-QR-A6GZ TCGA-QR-A6H2 TCGA-QR-A6H5 TCGA-QR-A6ZZ TCGA-QR-A700 
        1.05        30.51         9.93        31.53         1.58        32.15 
TCGA-QR-A703 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70J 
       38.37         4.11         1.15        69.67       116.19        13.12 
TCGA-QR-A70N TCGA-QR-A70R TCGA-QR-A7IN TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 
        1.41        14.20        12.39         1.81         0.79        13.08 
TCGA-RW-A67V TCGA-RW-A67X TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A8AZ TCGA-S7-A7WP 
       86.89         2.93        13.32         6.28         2.89        31.04 
TCGA-S7-A7WQ TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SA-A6C2 TCGA-SP-A6QH TCGA-SR-A6MR 
       26.96        12.66        18.94         9.73        72.43        79.20 
TCGA-SR-A6MS TCGA-SR-A6MV TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7UY TCGA-WB-A80L 
       81.93       121.05        25.15        25.32        10.65        34.26 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81I 
      127.56        19.59        32.88         5.98        24.16        22.32 
TCGA-WB-A821 TCGA-WB-A822 
       93.11       103.17 

$subtype4
TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X TCGA-QT-A5XO TCGA-RW-A685 TCGA-RW-A68G 
       23.11         2.33         6.02         2.30         0.85        41.88 
TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SR-A6MU TCGA-SR-A6MZ 
       35.51        27.91        20.58       111.25       110.53        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80K TCGA-WB-A816 TCGA-WB-A817 
       49.61        13.32        16.60        34.82        41.23        32.61 
TCGA-WB-A81H TCGA-WB-A81K TCGA-XG-A823 
       42.54        40.04        20.19 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.79     0.85 
subtype1 subtype2 subtype3 subtype4 
  316.73   114.77   137.59   111.25 
subtype1 subtype2 subtype3 subtype4 
  17.950   20.090   20.955   27.910 
[1] "0.1 - 316.7 (17.9)" "0.1 - 114.8 (20.1)" "0.8 - 137.6 (21.0)"
[4] "0.8 - 111.2 (27.9)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 25 14
  subtype2 35 34
  subtype3 27 23
  subtype4 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   14
  subtype2   35   34
  subtype3   27   23
  subtype4   14    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       35       27       14
  MALE         14       34       23        7
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         7
  subtype2                                1     2                         3
  subtype3                                0     2                         6
  subtype4                                0     1                         4
          vv
clus       WHITE
  subtype1    28
  subtype2    62
  subtype3    42
  subtype4    16
D5V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   1        2        2        1
  BLACK OR AFRICAN AMERICAN               7        3        6        4
  WHITE                                  28       62       42       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1  2 26
  subtype2  1 56
  subtype3  0 40
  subtype4  2 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   26
  subtype2    1   56
  subtype3    0   40
  subtype4    2   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        0        2
  NOT HISPANIC OR LATINO       26       56       40       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"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 37  2
  subtype2 69  2
  subtype3 46  2
  subtype4 21  0
subtype1 subtype2 subtype3 subtype4 
      39       71       48       21 
subtype1 subtype2 subtype3 subtype4 
       2        2        2        0 
$subtype1
TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GY 
       26.89        29.03         5.88        17.95        28.08         1.05 
TCGA-QR-A6H2 TCGA-QR-A700 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70E 
        9.93        32.15         1.15        69.67       116.19         6.31 
TCGA-QR-A70H TCGA-QR-A70R TCGA-QR-A70T TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RT-A6Y9 
       26.83        14.20         8.78        36.23         0.79       108.26 
TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A68D TCGA-RW-A8AZ TCGA-S7-A7WT 
       86.89        23.80        13.32        72.79         2.89        37.58 
TCGA-S7-A7WU TCGA-SA-A6C2 TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-W2-A7HH 
       30.51         9.73        79.20        81.93       106.75        25.61 
TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A81A 
       34.82         4.47       127.56        19.59         5.98        24.16 
TCGA-WB-A81E TCGA-WB-A81I TCGA-WB-A81M 
       37.18        22.32        45.83 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GW 
       31.46         2.27        81.70        35.01         1.25        16.14 
TCGA-QR-A6H1 TCGA-QR-A6H4 TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70K TCGA-QR-A70M 
       14.17        87.48         1.28        13.08         9.01        33.99 
TCGA-QR-A70O TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XM 
        3.65        48.43         0.07        41.79         6.94         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W 
       25.18         2.30         4.41        50.63         8.09        19.86 
TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        7.10         1.05         1.22        11.70        13.05         7.96 
TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
        1.78        20.09        31.59        30.21        37.25        40.70 
TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       25.32        18.08       114.77        82.62       110.04        15.52 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN 
        0.10        51.22        68.61        24.66         4.34        19.92 
TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF 
       14.20         1.18        19.86        12.03        12.49        17.69 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
        4.73         4.21        29.16        34.03        33.90        35.84 
TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       57.11        24.36        53.69        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       23.77        18.28        71.05        78.21        10.16 

$subtype3
TCGA-P8-A6RX TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 
       17.75       137.59        58.88        19.04        30.51         9.21 
TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A703 TCGA-QR-A705 
       14.27        31.53        15.58         1.58        38.37        10.42 
TCGA-QR-A706 TCGA-QR-A70D TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P 
        4.11         0.23        29.92        13.12         1.41       117.14 
TCGA-QR-A70Q TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RM-A68T 
        4.60        12.39        17.95         1.81        13.08        77.98 
TCGA-RM-A68W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A7CZ 
        0.92         2.93        33.30         6.28        15.02         4.41 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SP-A6QG 
       31.04        26.96        12.66        18.94       109.25        67.50 
TCGA-SP-A6QH TCGA-SR-A6MV TCGA-SR-A6MX TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 
       72.43       121.05         3.12        25.15        25.32        17.16 
TCGA-W2-A7UY TCGA-WB-A80P TCGA-WB-A814 TCGA-WB-A81G TCGA-WB-A821 TCGA-WB-A822 
       10.65       316.73        32.88        38.76        93.11       103.17 

$subtype4
TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X TCGA-RW-A685 TCGA-RW-A68G TCGA-S7-A7WO 
       23.11         2.33         6.02         0.85        41.88        35.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MU TCGA-SR-A6MZ 
       27.91        20.58       111.25         1.41       110.53        19.76 
TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80L TCGA-WB-A816 TCGA-WB-A817 
       49.61        13.32        16.60        34.26        41.23        32.61 
TCGA-WB-A81H TCGA-WB-A81K TCGA-XG-A823 
       42.54        40.04        20.19 

subtype1 subtype2 subtype3 subtype4 
    0.79     0.07     0.23     0.85 
subtype1 subtype2 subtype3 subtype4 
  127.56   114.77   316.73   111.25 
subtype1 subtype2 subtype3 subtype4 
  26.830   18.280   18.445   27.910 
[1] "0.8 - 127.6 (26.8)" "0.1 - 114.8 (18.3)" "0.2 - 316.7 (18.4)"
[4] "0.8 - 111.2 (27.9)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 23 16
  subtype2 41 30
  subtype3 23 25
  subtype4 14  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   16
  subtype2   41   30
  subtype3   23   25
  subtype4   14    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23       41       23       14
  MALE         16       30       25        7
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         4
  subtype2                                1     2                         5
  subtype3                                0     1                         8
  subtype4                                0     1                         3
          vv
clus       WHITE
  subtype1    33
  subtype2    60
  subtype3    38
  subtype4    17
D6V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   2        2        1        1
  BLACK OR AFRICAN AMERICAN               4        5        8        3
  WHITE                                  33       60       38       17
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1  1 29
  subtype2  2 55
  subtype3  0 38
  subtype4  2 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   29
  subtype2    2   55
  subtype3    0   38
  subtype4    2   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       29       55       38       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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 70  5
  subtype2 65  0
  subtype3 38  1
subtype1 subtype2 subtype3 
      75       65       39 
subtype1 subtype2 subtype3 
       5        0        1 
$subtype1
TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GU TCGA-QR-A6GX 
       26.89        29.03        17.75        17.95        58.88        19.04 
TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H4 TCGA-QR-A6H5 TCGA-QR-A6H6 
       30.51         9.21         9.93        87.48        31.53        15.58 
TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A708 
        1.58        32.15        38.37        10.42         4.11         1.15 
TCGA-QR-A70A TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N 
       69.67         0.23         6.31        29.92        13.12         1.41 
TCGA-QR-A70P TCGA-QR-A70Q TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL 
      117.14         4.60        12.39        17.95        36.23         1.81 
TCGA-QT-A7U0 TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 
       13.08         0.92       108.26         2.93        33.30        23.80 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WP 
        6.28        72.79        15.02         4.41         2.89        31.04 
TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SA-A6C2 TCGA-SP-A6QD 
       26.96        30.51        12.66        18.94         9.73       109.25 
TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SQ-A6I4 TCGA-SR-A6MP TCGA-SR-A6MR TCGA-SR-A6MT 
       67.50        72.43         1.41        51.22        79.20       106.75 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
      121.05         3.12        25.15        25.32        17.16         1.18 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y 
       25.61        10.65        34.82       316.73       127.56        19.59 
TCGA-WB-A814 TCGA-WB-A81A TCGA-WB-A81E TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81P 
       32.88        24.16        37.18        38.76        22.32        12.99 
TCGA-WB-A81Q TCGA-WB-A821 TCGA-WB-A822 
       24.82        93.11       103.17 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GW 
       31.46         2.27        81.70        35.01         1.25        16.14 
TCGA-QR-A6GY TCGA-QR-A6H1 TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70H TCGA-QR-A70K 
        1.05        14.17         1.28        13.08        26.83         9.01 
TCGA-QR-A70M TCGA-QR-A70O TCGA-QR-A70T TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W 
       33.99         3.65         8.78        48.43         0.07        41.79 
TCGA-QR-A70X TCGA-QT-A5XK TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W 
        6.02         6.94        25.18        50.63         8.09        19.86 
TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        7.10         1.05         1.22        11.70        13.05         7.96 
TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR 
        1.78        20.09        31.59        30.21        37.25        40.70 
TCGA-S7-A7WT TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       37.58        18.08       114.77        82.62       110.04        15.52 
TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H5 
        0.10        68.61        24.66         4.34        19.92        14.20 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-WB-A80M TCGA-WB-A80N 
       19.86        12.03        12.49        17.69         4.47         4.73 
TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J 
       29.16        34.03        33.90        35.84        57.11        24.36 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A81W 
       45.83        53.69         1.61        71.05        78.21 

$subtype3
TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6H3 TCGA-QR-A70C 
        5.88        28.08        23.11       137.59        14.27       116.19 
TCGA-QR-A70G TCGA-QR-A70R TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        2.33        14.20         0.72         2.30         4.41         0.79 
TCGA-RM-A68T TCGA-RW-A67V TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A68G TCGA-S7-A7WO 
       77.98        86.89         0.85        13.32        41.88        35.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-SP-A6QK TCGA-SR-A6MS TCGA-SR-A6MU 
       27.91        20.58        25.32       111.25        81.93       110.53 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A80L TCGA-WB-A80O 
       19.76        49.61        13.32        16.60        34.26         4.21 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81H TCGA-WB-A81K TCGA-WB-A81S 
        5.98        41.23        32.61        42.54        40.04        23.77 
TCGA-WB-A81T TCGA-WB-A820 TCGA-XG-A823 
       18.28        10.16        20.19 

subtype1 subtype2 subtype3 
    0.23     0.07     0.72 
subtype1 subtype2 subtype3 
  316.73   114.77   137.59 
subtype1 subtype2 subtype3 
   24.16    19.86    23.11 
[1] "0.2 - 316.7 (24.2)" "0.1 - 114.8 (19.9)" "0.7 - 137.6 (23.1)"
D7V2, continuous
D7V3, binary
          cls
clus        0  1
  subtype1 42 33
  subtype2 37 28
  subtype3 22 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   33
  subtype2   37   28
  subtype3   22   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42       37       22
  MALE         33       28       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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         9
  subtype2                                0     2                         5
  subtype3                                0     1                         6
          vv
clus       WHITE
  subtype1    61
  subtype2    55
  subtype3    32
D7V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   3        2        1
  BLACK OR AFRICAN AMERICAN               9        5        6
  WHITE                                  61       55       32
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1  1 60
  subtype2  2 50
  subtype3  2 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   60
  subtype2    2   50
  subtype3    2   28
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        2        2
  NOT HISPANIC OR LATINO       60       50       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 73  4
  subtype2 57  2
  subtype3 18  0
  subtype4 25  0
subtype1 subtype2 subtype3 subtype4 
      77       59       18       25 
subtype1 subtype2 subtype3 subtype4 
       4        2        0        0 
$subtype1
TCGA-P7-A5NX TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GT 
       26.89        29.03        17.75         5.88        17.95       137.59 
TCGA-QR-A6GU TCGA-QR-A6GX TCGA-QR-A6GZ TCGA-QR-A6H0 TCGA-QR-A6H2 TCGA-QR-A6H4 
       58.88        19.04        30.51         9.21         9.93        87.48 
TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A702 TCGA-QR-A703 
       31.53        15.58         1.58        32.15         1.28        38.37 
TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C TCGA-QR-A70D 
       10.42         4.11         1.15        69.67       116.19         0.23 
TCGA-QR-A70E TCGA-QR-A70J TCGA-QR-A70K TCGA-QR-A70N TCGA-QR-A70P TCGA-QR-A70Q 
        6.31        13.12         9.01         1.41       117.14         4.60 
TCGA-QR-A70T TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 
        8.78        12.39        17.95        36.23         1.81        13.08 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 
        0.92       108.26         2.93        33.30        23.80        13.32 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-RX-A8JQ 
        6.28        72.79        15.02         4.41         2.89        20.09 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SA-A6C2 
       31.04        26.96        30.51        12.66        18.94         9.73 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SQ-A6I4 TCGA-SR-A6MR TCGA-SR-A6MT 
      109.25        67.50        72.43         1.41        79.20       106.75 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7UY 
      121.05         3.12        25.15        25.32        17.16        10.65 
TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A81E 
       34.82       316.73       127.56        19.59        32.88        37.18 
TCGA-WB-A81G TCGA-WB-A81I TCGA-WB-A81P TCGA-WB-A821 TCGA-WB-A822 
       38.76        22.32        12.99        93.11       103.17 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GS TCGA-QR-A6GW 
       31.46         2.27        81.70        35.01         1.25        16.14 
TCGA-QR-A6H1 TCGA-QR-A70I TCGA-QR-A70M TCGA-QR-A70O TCGA-QR-A70U TCGA-QR-A70V 
       14.17        29.92        33.99         3.65        48.43         0.07 
TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W 
       41.79         6.94        25.18        50.63         8.09        19.86 
TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A7D0 
        7.10         1.05         1.22        13.05         7.96         1.78 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC 
       31.59        30.21        37.25        25.32        18.08       114.77 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       82.62       110.04        15.52         0.10        51.22        68.61 
TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HC 
       24.66         4.34        19.92        14.20         1.18        12.03 
TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A818 
       12.49        17.69        25.61         4.21        29.16        34.03 
TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81Q 
       33.90        35.84        57.11        24.36        53.69        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
        1.61        23.77        71.05        78.21        10.16 

$subtype3
TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A70H TCGA-QR-A70R TCGA-QT-A5XM TCGA-QT-A5XP 
       28.08         1.05        26.83        14.20         0.72         4.41 
TCGA-QT-A69Q TCGA-RW-A67V TCGA-RW-A68G TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MS 
        0.79        86.89        41.88        40.70        37.58        81.93 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M 
       34.26         4.47         5.98        24.16        40.04        45.83 

$subtype4
TCGA-QR-A6GR TCGA-QR-A6H3 TCGA-QR-A707 TCGA-QR-A70G TCGA-QR-A70X TCGA-QT-A5XO 
       23.11        14.27        13.08         2.33         6.02         2.30 
TCGA-RM-A68T TCGA-RW-A685 TCGA-RW-A689 TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW 
       77.98         0.85        11.70        35.51        27.91        20.58 
TCGA-SP-A6QK TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HB 
      111.25       110.53        19.76        49.61        13.32        19.86 
TCGA-W2-A7HE TCGA-WB-A80N TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81H TCGA-WB-A81T 
       16.60         4.73        41.23        32.61        42.54        18.28 
TCGA-XG-A823 
       20.19 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.07     0.72     0.85 
subtype1 subtype2 subtype3 subtype4 
  316.73   114.77    86.89   111.25 
subtype1 subtype2 subtype3 subtype4 
  19.590   24.360   27.455   19.860 
[1] "0.2 - 316.7 (19.6)" "0.1 - 114.8 (24.4)" "0.7 - 86.9 (27.5)" 
[4] "0.8 - 111.2 (19.9)"
D8V2, continuous
D8V3, binary
          cls
clus        0  1
  subtype1 42 35
  subtype2 35 24
  subtype3  9  9
  subtype4 15 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   35
  subtype2   35   24
  subtype3    9    9
  subtype4   15   10
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       35        9       15
  MALE         35       24        9       10
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        10
  subtype2                                1     2                         4
  subtype3                                0     0                         1
  subtype4                                0     1                         5
          vv
clus       WHITE
  subtype1    63
  subtype2    49
  subtype3    17
  subtype4    19
D8V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   3        2        0        1
  BLACK OR AFRICAN AMERICAN              10        4        1        5
  WHITE                                  63       49       17       19
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1  1 61
  subtype2  2 45
  subtype3  0 12
  subtype4  2 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   61
  subtype2    2   45
  subtype3    0   12
  subtype4    2   20
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       61       45       12       20
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 36  0
  subtype2 62  2
  subtype3 11  1
  subtype4 40  2
  subtype5 23  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      36       64       12       42       24 
subtype1 subtype2 subtype3 subtype4 subtype5 
       0        2        1        2        1 
$subtype1
TCGA-P7-A5NX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QR-A6GX TCGA-QR-A6GY 
       26.89         5.88        17.95        28.08        19.04         1.05 
TCGA-QR-A702 TCGA-QR-A70H TCGA-QR-A70R TCGA-QR-A70T TCGA-QT-A5XJ TCGA-QT-A5XM 
        1.28        26.83        14.20         8.78        36.23         0.72 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67Y 
        4.41         0.79       108.26        50.63        86.89         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A68F TCGA-RW-A68G TCGA-S7-A7WR TCGA-S7-A7WT 
       33.30        23.80        15.02        41.88        40.70        37.58 
TCGA-S7-A7WU TCGA-SA-A6C2 TCGA-SR-A6MS TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       30.51         9.73        81.93        34.82        34.26         4.47 
TCGA-WB-A80Q TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81S 
      127.56         5.98        24.16        40.04        45.83        23.77 

$subtype2
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-PR-A5PG TCGA-QR-A6GO TCGA-QR-A6GW TCGA-QR-A6H1 
       31.46         2.27        81.70        35.01        16.14        14.17 
TCGA-QR-A707 TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70O TCGA-QR-A70U TCGA-QR-A70V 
       13.08         9.01        33.99         3.65        48.43         0.07 
TCGA-QR-A70W TCGA-QR-A70X TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-RT-A6YC 
       41.79         6.02         6.94        25.18         2.30         8.09 
TCGA-RW-A67W TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
       19.86         1.05         0.85         1.22        11.70        13.05 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7X2 TCGA-SP-A6QC 
       20.09        31.59        30.21        37.25        18.08       114.77 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       82.62       110.04        15.52       111.25         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MU TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ 
       51.22        68.61       110.53        24.66        19.76         4.34 
TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
       19.92        14.20        19.86        12.03        12.49        16.60 
TCGA-W2-A7HF TCGA-WB-A80N TCGA-WB-A80V TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
       17.69         4.73        29.16        34.03        33.90        35.84 
TCGA-WB-A81F TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       57.11        24.36        53.69        12.99        24.82         1.61 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A820 
       18.28        71.05        78.21        10.16 

$subtype3
TCGA-P8-A5KC TCGA-QR-A6GS TCGA-QR-A6H4 TCGA-QR-A70C TCGA-QR-A70J TCGA-QT-A7U0 
       29.03         1.25        87.48       116.19        13.12        13.08 
TCGA-RW-A68B TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-S7-A7WX TCGA-W2-A7HA TCGA-WB-A80O 
        7.96         1.78         2.89        25.32         1.18         4.21 

$subtype4
TCGA-P8-A6RX TCGA-QR-A6GU TCGA-QR-A6GZ TCGA-QR-A6H2 TCGA-QR-A6H3 TCGA-QR-A6H5 
       17.75        58.88        30.51         9.93        14.27        31.53 
TCGA-QR-A6ZZ TCGA-QR-A700 TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A708 
        1.58        32.15        38.37        10.42         4.11         1.15 
TCGA-QR-A70A TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70N TCGA-QR-A70P 
       69.67         0.23         6.31        29.92         1.41       117.14 
TCGA-QR-A70Q TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XL TCGA-RW-A67X TCGA-RW-A686 
        4.60        12.39        17.95         1.81         2.93        13.32 
TCGA-RW-A68D TCGA-RW-A7CZ TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7X0 TCGA-S7-A7X1 
       72.79         4.41        31.04        26.96        12.66        18.94 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SR-A6MR TCGA-SR-A6MT TCGA-SR-A6MV TCGA-TT-A6YP 
      109.25        67.50        79.20       106.75       121.05        25.32 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A81E TCGA-WB-A821 
       25.61        10.65        19.59        32.88        37.18        93.11 

$subtype5
TCGA-QR-A6GR TCGA-QR-A6GT TCGA-QR-A6H0 TCGA-QR-A6H6 TCGA-QR-A70G TCGA-RM-A68T 
       23.11       137.59         9.21        15.58         2.33        77.98 
TCGA-RM-A68W TCGA-RW-A68C TCGA-S7-A7WO TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QH 
        0.92         6.28        35.51        27.91        20.58        72.43 
TCGA-SR-A6MX TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-W2-A7H7 TCGA-WB-A80P 
        3.12        49.61        25.15        13.32        17.16       316.73 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A822 TCGA-XG-A823 
       41.23        32.61        38.76        42.54       103.17        20.19 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.72     0.07     1.18     0.23     0.92 
subtype1 subtype2 subtype3 subtype4 subtype5 
  127.56   114.77   116.19   121.05   316.73 
subtype1 subtype2 subtype3 subtype4 subtype5 
  25.495   19.810   10.520   22.455   26.530 
[1] "0.7 - 127.6 (25.5)" "0.1 - 114.8 (19.8)" "1.2 - 116.2 (10.5)"
[4] "0.2 - 121.0 (22.5)" "0.9 - 316.7 (26.5)"
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1 24 12
  subtype2 35 29
  subtype3  7  5
  subtype4 24 18
  subtype5 11 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   12
  subtype2   35   29
  subtype3    7    5
  subtype4   24   18
  subtype5   11   13
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       35        7       24       11
  MALE         12       29        5       18       13
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                0     3                         5
  subtype3                                1     0                         1
  subtype4                                0     2                         6
  subtype5                                0     1                         3
          vv
clus       WHITE
  subtype1    31
  subtype2    54
  subtype3     9
  subtype4    33
  subtype5    20
D9V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        3        0        2        1
  BLACK OR AFRICAN AMERICAN               5        5        1        6        3
  WHITE                                  31       54        9       33       20
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1  1 25
  subtype2  2 52
  subtype3  0  8
  subtype4  0 33
  subtype5  2 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   25
  subtype2    2   52
  subtype3    0    8
  subtype4    0   33
  subtype5    2   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        2        0        0        2
  NOT HISPANIC OR LATINO       25       52        8       33       19
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 77  3
  subtype2 58  3
  subtype3 18  0
  subtype4 19  0
subtype1 subtype2 subtype3 subtype4 
      80       61       18       19 
subtype1 subtype2 subtype3 subtype4 
       3        3        0        0 
$subtype1
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PG TCGA-QR-A6GO 
       26.89        31.46         2.27         5.88        81.70        35.01 
TCGA-QR-A6GS TCGA-QR-A6GW TCGA-QR-A6GX TCGA-QR-A6H1 TCGA-QR-A6H2 TCGA-QR-A6H4 
        1.25        16.14        19.04        14.17         9.93        87.48 
TCGA-QR-A702 TCGA-QR-A707 TCGA-QR-A70K TCGA-QR-A70M TCGA-QR-A70O TCGA-QR-A70T 
        1.28        13.08         9.01        33.99         3.65         8.78 
TCGA-QR-A70U TCGA-QR-A70V TCGA-QR-A70W TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO 
       48.43         0.07        41.79         6.94        25.18         2.30 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A681 
      108.26        50.63         8.09        19.86         7.10        23.80 
TCGA-RW-A684 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68F TCGA-RW-A7D0 
        1.05         1.22        13.05         7.96        15.02         1.78 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WU TCGA-S7-A7WX 
       20.09        31.59        30.21        37.25        30.51        25.32 
TCGA-S7-A7X2 TCGA-SA-A6C2 TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ 
       18.08         9.73       114.77        82.62       110.04        15.52 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MY TCGA-TT-A6YJ 
        1.41         0.10        68.61       106.75        24.66         4.34 
TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       19.92        14.20         1.18        19.86        12.03        12.49 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V 
       17.69        25.61        34.82         4.73         4.21        29.16 
TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D TCGA-WB-A81F TCGA-WB-A81J 
       19.59        34.03        33.90        35.84        57.11        24.36 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81V 
       53.69        12.99        24.82         1.61        23.77        71.05 
TCGA-WB-A81W TCGA-WB-A820 
       78.21        10.16 

$subtype2
TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QR-A6GT TCGA-QR-A6GU TCGA-QR-A6GZ 
       29.03        17.75        17.95       137.59        58.88        30.51 
TCGA-QR-A6H0 TCGA-QR-A6H3 TCGA-QR-A6H5 TCGA-QR-A6H6 TCGA-QR-A6ZZ TCGA-QR-A700 
        9.21        14.27        31.53        15.58         1.58        32.15 
TCGA-QR-A703 TCGA-QR-A705 TCGA-QR-A706 TCGA-QR-A708 TCGA-QR-A70A TCGA-QR-A70C 
       38.37        10.42         4.11         1.15        69.67       116.19 
TCGA-QR-A70D TCGA-QR-A70E TCGA-QR-A70I TCGA-QR-A70J TCGA-QR-A70N TCGA-QR-A70P 
        0.23         6.31        29.92        13.12         1.41       117.14 
TCGA-QR-A70Q TCGA-QR-A7IN TCGA-QR-A7IP TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A7U0 
        4.60        12.39        17.95        36.23         1.81        13.08 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A686 TCGA-RW-A68C 
       77.98         0.92         2.93        33.30        13.32         6.28 
TCGA-RW-A68D TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7X0 
       72.79         4.41         2.89        31.04        26.96        12.66 
TCGA-S7-A7X1 TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SR-A6MP TCGA-SR-A6MR 
       18.94       109.25        67.50        72.43        51.22        79.20 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7UY 
      121.05         3.12        25.15        25.32        17.16        10.65 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A814 TCGA-WB-A81E TCGA-WB-A81G TCGA-WB-A821 
      316.73       127.56        32.88        37.18        38.76        93.11 
TCGA-WB-A822 
      103.17 

$subtype3
TCGA-PR-A5PH TCGA-QR-A6GY TCGA-QR-A70H TCGA-QR-A70R TCGA-QT-A5XM TCGA-QT-A5XP 
       28.08         1.05        26.83        14.20         0.72         4.41 
TCGA-QT-A69Q TCGA-RW-A67V TCGA-RW-A68G TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SR-A6MS 
        0.79        86.89        41.88        40.70        37.58        81.93 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A815 TCGA-WB-A81A TCGA-WB-A81K TCGA-WB-A81M 
       34.26         4.47         5.98        24.16        40.04        45.83 

$subtype4
TCGA-QR-A6GR TCGA-QR-A70G TCGA-QR-A70X TCGA-RW-A685 TCGA-RW-A689 TCGA-S7-A7WO 
       23.11         2.33         6.02         0.85        11.70        35.51 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QK TCGA-SR-A6MU TCGA-SR-A6MZ TCGA-SR-A6N0 
       27.91        20.58       111.25       110.53        19.76        49.61 
TCGA-TT-A6YO TCGA-W2-A7HE TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81H TCGA-WB-A81T 
       13.32        16.60        41.23        32.61        42.54        18.28 
TCGA-XG-A823 
       20.19 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.23     0.72     0.85 
subtype1 subtype2 subtype3 subtype4 
  114.77   316.73    86.89   111.25 
subtype1 subtype2 subtype3 subtype4 
  19.725   25.320   27.455   20.580 
[1] "0.1 - 114.8 (19.7)" "0.2 - 316.7 (25.3)" "0.7 - 86.9 (27.5)" 
[4] "0.8 - 111.2 (20.6)"
D10V2, continuous
D10V3, binary
          cls
clus        0  1
  subtype1 48 32
  subtype2 31 30
  subtype3  9  9
  subtype4 13  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   32
  subtype2   31   30
  subtype3    9    9
  subtype4   13    6
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       48       31        9       13
  MALE         32       30        9        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         7
  subtype2                                0     2                         9
  subtype3                                0     0                         1
  subtype4                                0     1                         3
          vv
clus       WHITE
  subtype1    66
  subtype2    49
  subtype3    17
  subtype4    15
D10V4, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   3        2        0        1
  BLACK OR AFRICAN AMERICAN               7        9        1        3
  WHITE                                  66       49       17       15
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  3 62
  subtype2  0 49
  subtype3  0 12
  subtype4  2 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   62
  subtype2    0   49
  subtype3    0   12
  subtype4    2   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        0        2
  NOT HISPANIC OR LATINO       62       49       12       14
[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"
