[1] "ofn"        "-oTTGCT-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/TGCT-TP/22507091/TGCT-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.mergedcluster.txt"

nPatients in clinical file=134, in cluster file=150, common to both=134
[1]  10 134
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
43 33 45 13 
 1  2  3  4 
43 33 45 13 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
43 20 32 39 
 1  2  3  4 
43 20 32 39 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
44  7  8 29 16 
 1  2  3  4  5 
44  7  8 29 16 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
50 19 35 
 1  2  3 
50 19 35 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6  7 
33 30 30 17  8 15  1 
 1  2  3  4  5  6 
33 30 30 17  8 15 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
42 27 10 17  8 20 10 
 1  2  3  4  5  6  7 
42 27 10 17  8 20 10 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
50 55 29 
 1  2  3 
50 55 29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
69 36 29 
 1  2  3 
69 36 29 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
68 34 32 
 1  2  3 
68 34 32 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
33 36 17 19 19 10 
 1  2  3  4  5  6 
33 36 17 19 19 10 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 134 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=4,	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=130,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 134 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "RADIATION_THERAPY"          
[7] "KARNOFSKY_PERFORMANCE_SCORE" "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=38, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 
76 51  6 
[1] "table(vv)"
vv
T1 T2 T3 
76 51  6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
76 51  6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
76 51  6 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
46 11  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   46    13 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
46 11  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 46

$Class1_nSamples
[1] 13

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   46    13 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=3, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 41  2
  subtype2 33  0
  subtype3 43  2
  subtype4 13  0
subtype1 subtype2 subtype3 subtype4 
      43       33       45       13 
subtype1 subtype2 subtype3 subtype4 
       2        0        2        0 
$subtype1
TCGA-2G-AAG0 TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAFL TCGA-2G-AAFM 
       50.27        26.66        20.32        46.13        24.66        16.54 
TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG5 TCGA-2G-AAGJ TCGA-2G-AAGP TCGA-2G-AAGZ 
       22.52        36.13        75.58        96.59       132.10       172.04 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHN TCGA-2G-AAKH TCGA-2X-A9D6 TCGA-4K-AA1H 
      110.10       182.10       211.89       225.60        19.96        17.03 
TCGA-4K-AA1I TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AD TCGA-VF-A8AE 
        0.10        37.68        24.99        35.61        33.07        23.90 
TCGA-W4-A7U3 TCGA-WZ-A7V4 TCGA-XE-A8H1 TCGA-XE-A8H4 TCGA-XE-AANV TCGA-XE-AAO4 
        4.90        29.39         6.87        18.38        55.92        12.07 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90S 
       16.87         8.88        67.66        41.69        15.48        31.92 
TCGA-YU-A94D TCGA-YU-AA4L TCGA-YU-AA61 TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0F 
       71.24        51.72        28.41        37.02        27.88        22.39 
TCGA-ZM-AA0H 
       57.07 

$subtype2
TCGA-2G-AAFE TCGA-2G-AAG3 TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 
      154.59        52.37        41.39        76.11       114.77       128.58 
TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAGS TCGA-2G-AAHL TCGA-2G-AAHT TCGA-2X-A9D5 
      203.28        45.21       158.33       232.80        17.82        14.30 
TCGA-4K-AAAL TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP 
       15.88         9.14        13.58         1.38        16.31        17.75 
TCGA-VF-A8A9 TCGA-W4-A7U2 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-AANJ 
       36.79        41.52        34.88        25.45        40.01        65.98 
TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W 
       93.93         7.89         0.43         9.24        64.57        36.59 
TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       49.25        27.55        20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFJ TCGA-2G-AAFN TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG6 
       22.19        26.04        25.41        45.67        44.48        73.35 
TCGA-2G-AAG7 TCGA-2G-AAG9 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGG 
       81.37        73.45        84.99        81.47        89.88        85.84 
TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGT TCGA-2G-AAGV 
      103.13       119.05       127.92       120.20       144.85       148.83 
TCGA-2G-AAGW TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAHG 
      161.06       181.28       175.20       199.23       204.16        59.80 
TCGA-2G-AAKG TCGA-2G-AAKM TCGA-2G-AAL5 TCGA-2G-AAL7 TCGA-2G-AALP TCGA-S6-A8JX 
      216.92       229.22       244.50       131.21        86.96        18.15 
TCGA-SN-A84W TCGA-SN-A84X TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-X3-A8G4 
        9.63        10.26        17.23        37.18        24.26        28.14 
TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AAOJ TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       23.28        34.22        50.96        22.09        27.72        68.02 
TCGA-YU-A90Y TCGA-YU-A912 TCGA-YU-A94I 
        0.56        28.47        17.62 

$subtype4
TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGO TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 
       75.25        80.19       132.36       180.07        59.90        73.91 
TCGA-2G-AAHP TCGA-2G-AAKD TCGA-2G-AAKL TCGA-4K-AA1G TCGA-S6-A8JW TCGA-WZ-A7V3 
      186.31       208.44       230.89        14.33        22.95        24.76 
TCGA-XE-AANR 
        0.46 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.43     0.56     0.46 
subtype1 subtype2 subtype3 subtype4 
  225.60   232.80   244.50   230.89 
subtype1 subtype2 subtype3 subtype4 
   31.92    36.79    73.35    75.25 
[1] "0.1 - 225.6 (31.9)" "0.4 - 232.8 (36.8)" "0.6 - 244.5 (73.3)"
[4] "0.5 - 230.9 (75.2)"
D1V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1  9       4       15        5        1         4         0         1
  subtype2 11       7        6        3        0         1         1         0
  subtype3 21       4        5        2        2         0         0         0
  subtype4  5       3        0        1        1         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          1          1          1
  subtype2         0          0          1          0
  subtype3         1          0          4          3
  subtype4         1          0          0          1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  IS                9       11       21        5
  STAGE I           4        7        4        3
  STAGE IA         15        6        5        0
  STAGE IB          5        3        2        1
  STAGE II          1        0        2        1
  STAGE IIA         4        1        0        1
  STAGE IIB         0        1        0        0
  STAGE IIC         1        0        0        0
  STAGE III         0        0        1        1
  STAGE IIIA        1        0        0        0
  STAGE IIIB        1        1        4        0
  STAGE IIIC        1        0        3        1
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 27 13  2
  subtype2 21 11  1
  subtype3 25 17  3
  subtype4  3 10  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       27       21       25        3
  T2       13       11       17       10
  T3        2        1        3        0
[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"
          vv
clus       N0 N1+N2
  subtype1 11     5
  subtype2 10     3
  subtype3 21     4
  subtype4  4     1
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11       10       21        4
  N1+N2        5        3        4        1
[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"
D1V6, binary
          cls
clus        0  1
  subtype1 36  1
  subtype2 29  0
  subtype3 38  3
  subtype4 12  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    1
  subtype2   29    0
  subtype3   38    3
  subtype4   12    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36       29       38       12
  1        1        0        3        0
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 38  5
  subtype2 19 13
  subtype3 43  2
  subtype4 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    5
  subtype2   19   13
  subtype3   43    2
  subtype4   11    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        38       19       43       11
  YES        5       13        2        1
[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"
D1V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         3    36
  subtype2     1                         1    29
  subtype3     1                         2    41
  subtype4     0                         0    13
D1V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        1        0
  BLACK OR AFRICAN AMERICAN        3        1        2        0
  WHITE                           36       29       41       13
[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"
D1V10, binary
          cls
clus        0  1
  subtype1  3 35
  subtype2  3 28
  subtype3  5 36
  subtype4  1 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   35
  subtype2    3   28
  subtype3    5   36
  subtype4    1   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        3        5        1
  NOT HISPANIC OR LATINO       35       28       36       12
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 41  2
  subtype2 20  0
  subtype3 30  2
  subtype4 39  0
subtype1 subtype2 subtype3 subtype4 
      43       20       32       39 
subtype1 subtype2 subtype3 subtype4 
       2        0        2        0 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
      154.59        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG9 TCGA-2G-AAGP TCGA-2G-AAGZ 
       16.54        22.52        36.13        73.45       132.10       172.04 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 
      110.10       182.10       232.80       211.89        17.82        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-SB-A6J6 TCGA-VF-A8A9 TCGA-VF-A8AA 
       19.96        17.03         0.10        13.58        36.79        37.68 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-WZ-A7V3 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 
       35.61        23.90        24.76        29.39        34.88        25.45 
TCGA-XE-A8H4 TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOB TCGA-XE-AAOD TCGA-XE-AAOF 
       18.38        55.92        12.07        16.87        67.66        41.69 
TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90S TCGA-ZM-AA05 TCGA-ZM-AA0D TCGA-ZM-AA0F 
       15.48         9.24        31.92        37.02        27.88        22.39 
TCGA-ZM-AA0H 
       57.07 

$subtype2
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAH0 TCGA-2G-AAH3 
      114.77       128.58       203.28        45.21       180.07        59.90 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-SN-A6IS TCGA-SN-A84X TCGA-VF-A8AB TCGA-W4-A7U2 
       59.80       186.31        16.31        10.26        24.99        41.52 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-ZM-AA06 
       23.28        65.98         0.46        93.93         7.89        49.25 
TCGA-ZM-AA0B TCGA-ZM-AA0N 
       27.55        20.84 

$subtype3
TCGA-2G-AAG0 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFN TCGA-2G-AAG7 TCGA-2G-AAG8 
       50.27        22.19        24.66        25.41        81.37        75.25 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        84.99        81.47        89.88        96.59       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH 
      120.20       132.36       161.06       208.44       216.92       225.60 
TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 
      230.89       229.22       131.21        86.96        17.23        37.18 
TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-XE-A8H1 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
       33.07        24.26         6.87        22.09        27.72        68.02 
TCGA-YU-A90Y TCGA-YU-AA4L 
        0.56        51.72 

$subtype4
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       52.37        26.04        45.67        44.48        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84       103.13       127.92       158.33       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAH8 TCGA-2G-AAL5 
      181.28       175.20       199.23       204.16        73.91       244.50 
TCGA-4K-AA1G TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A76C 
       14.33        15.88        22.95        18.15         9.14         1.38 
TCGA-SN-A84W TCGA-SO-A8JP TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-A8H5 TCGA-XE-AANI 
        9.63        17.75         4.90        28.14        40.01        34.22 
TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-XE-AAOL TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 
        8.88        50.96         0.43        64.57        36.59        28.47 
TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA61 
       71.24        17.62        28.41 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.46     0.56     0.43 
subtype1 subtype2 subtype3 subtype4 
  232.80   203.28   230.89   244.50 
subtype1 subtype2 subtype3 subtype4 
   31.92    47.23    80.78    44.48 
[1] "0.1 - 232.8 (31.9)" "0.5 - 203.3 (47.2)" "0.6 - 230.9 (80.8)"
[4] "0.4 - 244.5 (44.5)"
D2V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1  8       9       14        3        0         5         0         1
  subtype2  7       4        5        2        0         0         1         0
  subtype3 12       2        3        4        3         1         0         0
  subtype4 19       3        4        2        1         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          1          1          0
  subtype2         0          0          0          0
  subtype3         1          0          3          2
  subtype4         1          0          2          3
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  IS                8        7       12       19
  STAGE I           9        4        2        3
  STAGE IA         14        5        3        4
  STAGE IB          3        2        4        2
  STAGE II          0        0        3        1
  STAGE IIA         5        0        1        0
  STAGE IIB         0        1        0        0
  STAGE IIC         1        0        0        0
  STAGE III         0        0        1        1
  STAGE IIIA        1        0        0        0
  STAGE IIIB        1        0        3        2
  STAGE IIIC        0        0        2        3
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 26 14  2
  subtype2 11  9  0
  subtype3 12 19  1
  subtype4 27  9  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       26       11       12       27
  T2       14        9       19        9
  T3        2        0        1        3
[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"
          vv
clus       N0 N1+N2
  subtype1 11     7
  subtype2  6     1
  subtype3 15     3
  subtype4 14     2
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          11        6       15       14
  N1+N2        7        1        3        2
[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"
D2V6, binary
          cls
clus        0  1
  subtype1 38  1
  subtype2 19  0
  subtype3 28  1
  subtype4 30  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    1
  subtype2   19    0
  subtype3   28    1
  subtype4   30    2
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       38       19       28       30
  1        1        0        1        2
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 31 12
  subtype2 12  7
  subtype3 32  0
  subtype4 36  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   12
  subtype2   12    7
  subtype3   32    0
  subtype4   36    2
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        31       12       32       36
  YES       12        7        0        2
[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"
D2V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    40
  subtype2     1                         1    18
  subtype3     0                         3    29
  subtype4     1                         2    32
D2V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        1
  BLACK OR AFRICAN AMERICAN        0        1        3        2
  WHITE                           40       18       29       32
[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"
D2V10, binary
          cls
clus        0  1
  subtype1  1 41
  subtype2  5 15
  subtype3  2 27
  subtype4  4 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2    5   15
  subtype3    2   27
  subtype4    4   28
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        5        2        4
  NOT HISPANIC OR LATINO       41       15       27       28
[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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 43  1
  subtype2  7  0
  subtype3  8  0
  subtype4 27  2
  subtype5 15  1
subtype1 subtype2 subtype3 subtype4 subtype5 
      44        7        8       29       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        0        0        2        1 
$subtype1
TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 
       26.66        20.32        41.39        46.13        76.11       114.77 
TCGA-2G-AAF8 TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHG 
      128.58       180.07        59.90        73.91       110.10        59.80 
TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      232.80       186.31        17.82        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS 
       17.03         0.10        22.95        18.15         9.14        16.31 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-XE-A8H5 
       17.75        36.79        37.68        23.90        41.52        40.01 
TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 
       65.98         0.46        55.92        93.93        12.07         7.89 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 
       41.69         0.43         9.24        64.57        36.59        28.47 
TCGA-ZM-AA0B TCGA-ZM-AA0D 
       27.55        27.88 

$subtype2
TCGA-2G-AAFG TCGA-2G-AAFY TCGA-2G-AAG9 TCGA-2G-AAHC TCGA-XY-A89B TCGA-YU-A90S 
      203.28        36.13        73.45       182.10        15.48        31.92 
TCGA-ZM-AA05 
       37.02 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAG5 TCGA-2G-AAG8 TCGA-2G-AAGO TCGA-2G-AAGP 
       22.19        24.66        75.58        75.25       132.36       132.10 
TCGA-2G-AAGZ TCGA-XE-AAOD 
      172.04        67.66 

$subtype4
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFZ TCGA-2G-AAG6 TCGA-2G-AAGC TCGA-2G-AAGF 
       52.37        26.04        44.48        73.35        84.99        89.88 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM TCGA-2G-AAGS TCGA-2G-AAGV 
       85.84       103.13       119.05       127.92       158.33       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       204.16       216.92       244.50        86.96 
TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-A9SE TCGA-XE-AANI TCGA-XE-AAOB 
       10.26         4.90        28.14        23.28        34.22        16.87 
TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A90Y TCGA-YU-A94I TCGA-YU-AA61 
        8.88        50.96         0.56        17.62        28.41 

$subtype5
TCGA-2G-AAG0 TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAG7 TCGA-2G-AAGJ TCGA-2G-AAGN 
       50.27        16.54        25.41        81.37        96.59       120.20 
TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      144.85       161.06       225.60       230.89       229.22       131.21 
TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-XE-A8H1 TCGA-YU-A90P 
       37.18        24.26         6.87        68.02 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10    15.48    22.19     0.56     6.87 
subtype1 subtype2 subtype3 subtype4 subtype5 
  232.80   203.28   172.04   244.50   230.89 
subtype1 subtype2 subtype3 subtype4 subtype5 
  32.530   37.020   75.415   73.350   88.980 
[1] "0.1 - 232.8 (32.5)"  "15.5 - 203.3 (37.0)" "22.2 - 172.0 (75.4)"
[4] "0.6 - 244.5 (73.3)"  "6.9 - 230.9 (89.0)" 
D3V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1 14      11       12        4        0         0         0         0
  subtype2  2       0        2        0        0         1         1         0
  subtype3  2       0        0        4        0         1         0         0
  subtype4 14       2        4        0        1         0         0         1
  subtype5  6       0        3        0        3         1         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1          0          0          2
  subtype2          0          1          0
  subtype3          1          0          0
  subtype4          0          2          2
  subtype5          0          2          0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  IS               14        2        2       14        6
  STAGE I          11        0        0        2        0
  STAGE IA         12        2        0        4        3
  STAGE IB          4        0        4        0        0
  STAGE II          0        0        0        1        3
  STAGE IIA         0        1        1        0        1
  STAGE IIC         0        1        0        0        0
  STAGE III         0        0        0        1        0
  STAGE IIIA        0        0        1        0        0
  STAGE IIIB        0        1        0        2        2
  STAGE IIIC        2        0        0        2        0
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 29 15  0
  subtype2  4  3  0
  subtype3  1  7  0
  subtype4 21  5  3
  subtype5  6 10  0
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       29        4        1       21        6
  T2       15        3        7        5       10
  T3        0        0        0        3        0
[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"
          vv
clus       N0 N1+N2
  subtype1 16     0
  subtype2  1     2
  subtype3  5     2
  subtype4 12     2
  subtype5  6     3
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          16        1        5       12        6
  N1+N2        0        2        2        2        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 40  0
  subtype2  6  0
  subtype3  7  1
  subtype4 22  3
  subtype5 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    0
  subtype2    6    0
  subtype3    7    1
  subtype4   22    3
  subtype5   15    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       40        6        7       22       15
  1        0        0        1        3        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 29 13
  subtype2  5  2
  subtype3  8  0
  subtype4 28  1
  subtype5 16  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   13
  subtype2    5    2
  subtype3    8    0
  subtype4   28    1
  subtype5   16    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        29        5        8       28       16
  YES       13        2        0        1        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    36
  subtype2     0                         0     7
  subtype3     0                         0     8
  subtype4     1                         1    26
  subtype5     0                         1    15
D3V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        0        0        1        0
  BLACK OR AFRICAN AMERICAN        2        0        0        1        1
  WHITE                           36        7        8       26       15
[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"
D3V10, binary
          cls
clus        0  1
  subtype1  5 36
  subtype2  0  6
  subtype3  0  8
  subtype4  4 21
  subtype5  1 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   36
  subtype2    0    6
  subtype3    0    8
  subtype4    4   21
  subtype5    1   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        0        0        4        1
  NOT HISPANIC OR LATINO       36        6        8       21       14
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 49  1
  subtype2 19  0
  subtype3 32  3
subtype1 subtype2 subtype3 
      50       19       35 
subtype1 subtype2 subtype3 
       1        0        3 
$subtype1
TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 TCGA-2G-AAF6 
       26.66        20.32        41.39        46.13        76.11       114.77 
TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH3 TCGA-2G-AAH8 
      128.58       203.28        73.45       180.07        59.90        73.91 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHP TCGA-2G-AAHT 
      110.10       182.10        59.80       232.80       186.31        17.82 
TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-S6-A8JW 
       14.30        19.96        14.33        17.03         0.10        22.95 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA 
       18.15         9.14        16.31        17.75        36.79        37.68 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-XE-A8H5 TCGA-XE-AANJ TCGA-XE-AANR TCGA-XE-AANV 
       23.90        41.52        40.01        65.98         0.46        55.92 
TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B 
       93.93        12.07         7.89        41.69         0.43        15.48 
TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 
        9.24        64.57        31.92        36.59        28.47        37.02 
TCGA-ZM-AA0B TCGA-ZM-AA0D 
       27.55        27.88 

$subtype2
TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAG8 TCGA-2G-AAGG 
       22.19        24.66        75.58        73.35        75.25        85.84 
TCGA-2G-AAGI TCGA-2G-AAGO TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGZ 
      103.13       132.36       132.10       148.83       181.28       172.04 
TCGA-2G-AALP TCGA-W4-A7U3 TCGA-XE-A8H1 TCGA-XE-AAOC TCGA-XE-AAOD TCGA-YU-A94I 
       86.96         4.90         6.87         8.88        67.66        17.62 
TCGA-YU-AA61 
       28.41 

$subtype3
TCGA-2G-AAG0 TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY 
       50.27        52.37        26.04        16.54        25.41        36.13 
TCGA-2G-AAFZ TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       44.48        81.37        84.99        89.88        96.59       119.05 
TCGA-2G-AAGM TCGA-2G-AAGN TCGA-2G-AAGS TCGA-2G-AAGT TCGA-2G-AAGW TCGA-2G-AAGY 
      127.92       120.20       158.33       144.85       161.06       175.20 
TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL5 
      204.16       216.92       225.60       230.89       229.22       244.50 
TCGA-2G-AAL7 TCGA-SN-A84X TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-X3-A8G4 TCGA-XE-A9SE 
      131.21        10.26        37.18        24.26        28.14        23.28 
TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-YU-A90P TCGA-YU-A90Y 
       34.22        16.87        50.96        68.02         0.56 

subtype1 subtype2 subtype3 
    0.10     4.90     0.56 
subtype1 subtype2 subtype3 
  232.80   181.28   244.50 
subtype1 subtype2 subtype3 
   36.69    75.25    81.37 
[1] "0.1 - 232.8 (36.7)" "4.9 - 181.3 (75.2)" "0.6 - 244.5 (81.4)"
D4V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIC STAGE III
  subtype1 16      11       14        4        0         0         1         0
  subtype2  6       0        3        4        0         1         0         0
  subtype3 16       2        4        0        4         2         0         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1          0          1          2
  subtype2          1          1          1
  subtype3          0          3          1
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  IS               16        6       16
  STAGE I          11        0        2
  STAGE IA         14        3        4
  STAGE IB          4        4        0
  STAGE II          0        0        4
  STAGE IIA         0        1        2
  STAGE IIC         1        0        0
  STAGE III         0        0        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        1        3
  STAGE IIIC        2        1        1
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 33 17  0
  subtype2 10  8  1
  subtype3 18 15  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       33       10       18
  T2       17        8       15
  T3        0        1        2
[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"
          vv
clus       N0 N1+N2
  subtype1 17     1
  subtype2  8     3
  subtype3 15     5
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          17        8       15
  N1+N2        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 45  0
  subtype2 13  3
  subtype3 32  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    0
  subtype2   13    3
  subtype3   32    1
   clus
vv  subtype1 subtype2 subtype3
  0       45       13       32
  1        0        3        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 33 15
  subtype2 19  0
  subtype3 34  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   15
  subtype2   19    0
  subtype3   34    1
     clus
vv    subtype1 subtype2 subtype3
  NO        33       19       34
  YES       15        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         2    42
  subtype2     0                         0    18
  subtype3     1                         2    32
D4V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        2        0        2
  WHITE                           42       18       32
[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"
D4V10, binary
          cls
clus        0  1
  subtype1  5 41
  subtype2  2 14
  subtype3  3 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   41
  subtype2    2   14
  subtype3    3   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        3
  NOT HISPANIC OR LATINO       41       14       30
[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 32  1
  subtype2 30  0
  subtype3 27  3
  subtype4 17  0
  subtype5  8  0
  subtype6 15  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      33       30       30       17        8       15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        0        3        0        0        0 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAG9 TCGA-2G-AAH3 
      154.59        26.66        20.32        46.13        73.45        59.90 
TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D5 
       73.91       110.10       232.80       211.89        17.82        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1I TCGA-S6-A8JW TCGA-SB-A76C TCGA-VF-A8AA 
       19.96        14.33         0.10        22.95         1.38        37.68 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOF 
       29.39        34.88        18.38        55.92        12.07        41.69 
TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 
       15.48        64.57        31.92        28.47        37.02        49.25 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       27.88        22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       41.39        76.11       114.77       128.58       203.28        45.21 
TCGA-2G-AAH0 TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHP TCGA-S6-A8JX TCGA-S6-A8JY 
      180.07       182.10        59.80       186.31        18.15         9.14 
TCGA-SB-A6J6 TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-W4-A7U2 
       13.58        16.31        17.75        36.79        23.90        41.52 
TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 
       24.76        25.45        40.01        23.28        65.98        93.93 
TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 TCGA-YU-A90W TCGA-ZM-AA0B TCGA-ZM-AA0N 
        7.89         0.43         9.24        36.59        27.55        20.84 

$subtype3
TCGA-2G-AAG0 TCGA-2G-AAFI TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG7 
       50.27        22.19        16.54        25.41        36.13        81.37 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGN 
       80.19        84.99        81.47        89.88        96.59       120.20 
TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKH TCGA-2G-AAKL 
      132.36       161.06       172.04       208.44       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      229.22       131.21        17.23        37.18        33.07        24.26 
TCGA-XE-A8H1 TCGA-XE-AAOB TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
        6.87        16.87        22.09        27.72        68.02         0.56 

$subtype4
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGP TCGA-2G-AAGS 
       52.37        26.04        75.58        73.35       132.10       158.33 
TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAL5 TCGA-SN-A84W 
      148.83       181.28       175.20       199.23       244.50         9.63 
TCGA-SN-A84X TCGA-XE-AANI TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A94D 
       10.26        34.22         8.88        50.96        71.24 

$subtype5
TCGA-2G-AAFL TCGA-2G-AAFO TCGA-2G-AAG8 TCGA-4K-AA1H TCGA-4K-AAAL TCGA-VF-A8AC 
       24.66        22.52        75.25        17.03        15.88        35.61 
TCGA-XE-AANR TCGA-XE-AAOD 
        0.46        67.66 

$subtype6
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGK TCGA-2G-AAGM 
       45.67        44.48        85.84       103.13       119.05       127.92 
TCGA-2G-AAGT TCGA-2G-AAH4 TCGA-2G-AAKG TCGA-2G-AALP TCGA-W4-A7U3 TCGA-X3-A8G4 
      144.85       204.16       216.92        86.96         4.90        28.14 
TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       17.62        51.72        28.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.43     0.56     8.88     0.46     4.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  232.80   203.28   230.89   244.50    75.25   216.92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  31.920   36.690   74.105   73.350   23.590   85.840 
[1] "0.1 - 232.8 (31.9)" "0.4 - 203.3 (36.7)" "0.6 - 230.9 (74.1)"
[4] "8.9 - 244.5 (73.3)" "0.5 - 75.2 (23.6)"  "4.9 - 216.9 (85.8)"
D5V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1  6       8        9        4        0         1         0         1
  subtype2 11       6        8        2        0         0         1         0
  subtype3 12       1        3        2        3         3         0         0
  subtype4  9       1        2        0        0         1         0         0
  subtype5  1       1        2        3        0         1         0         0
  subtype6  7       1        1        0        1         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          1          2
  subtype2         0          0          0          0
  subtype3         1          1          2          1
  subtype4         0          0          2          0
  subtype5         0          0          0          0
  subtype6         1          0          1          2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  IS                6       11       12        9        1        7
  STAGE I           8        6        1        1        1        1
  STAGE IA          9        8        3        2        2        1
  STAGE IB          4        2        2        0        3        0
  STAGE II          0        0        3        0        0        1
  STAGE IIA         1        0        3        1        1        0
  STAGE IIB         0        1        0        0        0        0
  STAGE IIC         1        0        0        0        0        0
  STAGE III         0        0        1        0        0        1
  STAGE IIIA        0        0        1        0        0        0
  STAGE IIIB        1        0        2        2        0        1
  STAGE IIIC        2        0        1        0        0        2
[1] 12  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 18 13  1
  subtype2 23  6  1
  subtype3 10 19  1
  subtype4 12  4  1
  subtype5  2  6  0
  subtype6 10  3  2
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       18       23       10       12        2       10
  T2       13        6       19        4        6        3
  T3        1        1        1        1        0        2
[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"
          vv
clus       N0 N1+N2
  subtype1  8     2
  subtype2  9     1
  subtype3 11     6
  subtype4  7     2
  subtype5  4     1
  subtype6  6     1
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0           8        9       11        7        4        6
  N1+N2        2        1        6        2        1        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 28  0
  subtype2 27  0
  subtype3 27  1
  subtype4 16  0
  subtype5  8  0
  subtype6  8  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   27    0
  subtype3   27    1
  subtype4   16    0
  subtype5    8    0
  subtype6    8    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       28       27       27       16        8        8
  1        0        0        1        0        0        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 25  8
  subtype2 16 13
  subtype3 30  0
  subtype4 17  0
  subtype5  7  0
  subtype6 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    8
  subtype2   16   13
  subtype3   30    0
  subtype4   17    0
  subtype5    7    0
  subtype6   15    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        25       16       30       17        7       15
  YES        8       13        0        0        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1    28
  subtype2     1                         1    27
  subtype3     0                         2    28
  subtype4     1                         0    15
  subtype5     0                         0     8
  subtype6     0                         1    13
D5V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        0        1        0
  BLACK OR AFRICAN AMERICAN        1        1        2        0        0
  WHITE                           28       27       28       15        8
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        1
  WHITE                           13
[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"
D5V10, binary
          cls
clus        0  1
  subtype1  1 29
  subtype2  4 25
  subtype3  2 26
  subtype4  4 12
  subtype5  1  7
  subtype6  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   29
  subtype2    4   25
  subtype3    2   26
  subtype4    4   12
  subtype5    1    7
  subtype6    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        4        2        4        1        0
  NOT HISPANIC OR LATINO       29       25       26       12        7       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(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 41  1
  subtype2 27  0
  subtype3  8  2
  subtype4 17  0
  subtype5  8  0
  subtype6 19  1
  subtype7 10  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      42       27       10       17        8       20       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       1        0        2        0        0        1        0 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAG9 TCGA-2G-AAH0 
      154.59        26.66        20.32        46.13        73.45       180.07 
TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN 
       59.90        73.91       110.10       182.10       232.80       211.89 
TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I 
       17.82        14.30        19.96        14.33        17.03         0.10 
TCGA-4K-AAAL TCGA-S6-A8JW TCGA-SB-A76C TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
       15.88        22.95         1.38        37.68        24.99        35.61 
TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-AANR TCGA-XE-AANV 
       29.39        34.88        25.45        18.38         0.46        55.92 
TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A89B TCGA-YU-A90Q TCGA-YU-A90S 
       12.07        67.66        41.69        15.48        64.57        31.92 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       28.47        37.02        49.25        27.88        22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH 
       41.39        76.11       114.77       128.58       203.28        45.21 
TCGA-2G-AAHG TCGA-2G-AAHP TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SN-A6IS 
       59.80       186.31        18.15         9.14        13.58        16.31 
TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-XE-A8H5 
       17.75        36.79        23.90        41.52        24.76        40.01 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A9T9 
       23.28        65.98        93.93         7.89         0.43         9.24 
TCGA-YU-A90W TCGA-ZM-AA0B TCGA-ZM-AA0N 
       36.59        27.55        20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAGC TCGA-2G-AAGK TCGA-2G-AAGS TCGA-2G-AAKG TCGA-2G-AALP 
       22.19        84.99       119.05       158.33       216.92        86.96 
TCGA-X3-A8G4 TCGA-XE-AAOB TCGA-XY-A8S3 TCGA-YU-A90Y 
       28.14        16.87        27.72         0.56 

$subtype4
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAG5 TCGA-2G-AAG6 TCGA-2G-AAGG TCGA-2G-AAGI 
       52.37        26.04        75.58        73.35        85.84       103.13 
TCGA-2G-AAGP TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAL5 
      132.10       148.83       181.28       175.20       199.23       244.50 
TCGA-SN-A84W TCGA-SN-A84X TCGA-XE-AANI TCGA-XE-AAOC TCGA-YU-A94D 
        9.63        10.26        34.22         8.88        71.24 

$subtype5
TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGZ 
       24.66        16.54        22.52        75.25        80.19       172.04 
TCGA-2G-AAKH TCGA-XE-A8H1 
      225.60         6.87 

$subtype6
TCGA-2G-AAG0 TCGA-2G-AAFN TCGA-2G-AAFY TCGA-2G-AAG7 TCGA-2G-AAGE TCGA-2G-AAGF 
       50.27        25.41        36.13        81.37        81.47        89.88 
TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAKD TCGA-2G-AAKL 
       96.59       120.20       132.36       161.06       208.44       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      229.22       131.21        17.23        37.18        33.07        24.26 
TCGA-XY-A8S2 TCGA-YU-A90P 
       22.09        68.02 

$subtype7
TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAH4 TCGA-W4-A7U3 
       45.67        44.48       127.92       144.85       204.16         4.90 
TCGA-XE-AAOJ TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        17.62        51.72        28.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.10     0.43     0.56     8.88     6.87    17.23     4.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  232.80   203.28   216.92   244.50   225.60   230.89   204.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  30.655   36.590   56.565   75.580   49.955   81.420   48.315 
[1] "0.1 - 232.8 (30.7)"  "0.4 - 203.3 (36.6)"  "0.6 - 216.9 (56.6)" 
[4] "8.9 - 244.5 (75.6)"  "6.9 - 225.6 (50.0)"  "17.2 - 230.9 (81.4)"
[7] "4.9 - 204.2 (48.3)" 
D6V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1  9       9       12        5        0         1         0         1
  subtype2  9       6        8        2        0         0         1         0
  subtype3  5       1        0        1        0         0         0         0
  subtype4  9       1        2        0        0         1         0         0
  subtype5  1       0        0        2        1         3         0         0
  subtype6  8       1        3        1        2         1         0         0
  subtype7  5       0        1        0        1         0         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          1          2
  subtype2         0          0          0          0
  subtype3         0          0          2          1
  subtype4         0          0          1          1
  subtype5         0          1          0          0
  subtype6         1          0          2          0
  subtype7         1          0          0          1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  IS                9        9        5        9        1        8        5
  STAGE I           9        6        1        1        0        1        0
  STAGE IA         12        8        0        2        0        3        1
  STAGE IB          5        2        1        0        2        1        0
  STAGE II          0        0        0        0        1        2        1
  STAGE IIA         1        0        0        1        3        1        0
  STAGE IIB         0        1        0        0        0        0        0
  STAGE IIC         1        0        0        0        0        0        0
  STAGE III         0        0        0        0        0        1        1
  STAGE IIIA        0        0        0        0        1        0        0
  STAGE IIIB        1        0        2        1        0        2        0
  STAGE IIIC        2        0        1        1        0        0        1
[1] 12  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 21 18  2
  subtype2 22  5  0
  subtype3  6  3  1
  subtype4 11  4  2
  subtype5  3  5  0
  subtype6  6 14  0
  subtype7  7  2  1
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       21       22        6       11        3        6        7
  T2       18        5        3        4        5       14        2
  T3        2        0        1        2        0        0        1
[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"
          vv
clus       N0 N1+N2
  subtype1 11     2
  subtype2  9     1
  subtype3  5     1
  subtype4  8     2
  subtype5  2     4
  subtype6  9     3
  subtype7  2     0
D6V5, multiclass
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      13       10        6       10        6       12        2 
 [1] "subtype1" "subtype6" "subtype1" "subtype2" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype4"
[13] "subtype5" "subtype5" "subtype6" "subtype5" "subtype6" "subtype4"
[19] "subtype4" "subtype6" "subtype5" "subtype1" "subtype5" "subtype3"
[25] "subtype6" "subtype6" "subtype4" "subtype4" "subtype6" "subtype3"
[31] "subtype6" "subtype6" "subtype4" "subtype3" "subtype6" "subtype4"
[37] "subtype4" "subtype5" "subtype4" "subtype2" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype3" "subtype4" "subtype6" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype6" "subtype2"
[55] "subtype1" "subtype1" "subtype3"
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          11        9        5        8        2        9
  N1+N2        2        1        1        2        4        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 37  0
  subtype2 24  0
  subtype3  8  1
  subtype4 15  1
  subtype5  7  1
  subtype6 19  0
  subtype7  5  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    0
  subtype2   24    0
  subtype3    8    1
  subtype4   15    1
  subtype5    7    1
  subtype6   19    0
  subtype7    5    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       37       24        8       15        7       19        5
  1        0        0        1        1        1        0        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 32  9
  subtype2 14 12
  subtype3 10  0
  subtype4 17  0
  subtype5  8  0
  subtype6 20  0
  subtype7 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32    9
  subtype2   14   12
  subtype3   10    0
  subtype4   17    0
  subtype5    8    0
  subtype6   20    0
  subtype7   10    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        32       14       10       17        8       20       10
  YES        9       12        0        0        0        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    36
  subtype2     1                         1    24
  subtype3     0                         1     9
  subtype4     1                         0    15
  subtype5     0                         0     8
  subtype6     0                         1    19
  subtype7     0                         1     8
D6V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            2        1        0        1        0
  BLACK OR AFRICAN AMERICAN        2        1        1        0        0
  WHITE                           36       24        9       15        8
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        1        1
  WHITE                           19        8
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
          cls
clus        0  1
  subtype1  2 37
  subtype2  4 22
  subtype3  0  9
  subtype4  3 13
  subtype5  1  7
  subtype6  1 18
  subtype7  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   37
  subtype2    4   22
  subtype3    0    9
  subtype4    3   13
  subtype5    1    7
  subtype6    1   18
  subtype7    1    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        4        0        3        1        1
  NOT HISPANIC OR LATINO       37       22        9       13        7       18
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO        5
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 49  1
  subtype2 53  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      50       55       29 
subtype1 subtype2 subtype3 
       1        2        1 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
      154.59        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAG9 TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC 
      114.77        73.45       180.07        73.91       110.10       182.10 
TCGA-2G-AAHG TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 
       59.80       232.80       211.89       186.31        17.82        14.30 
TCGA-2X-A9D6 TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JX TCGA-SB-A6J6 
       19.96        17.03         0.10        15.88        18.15        13.58 
TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8AA TCGA-VF-A8AB TCGA-VF-A8AC 
        1.38        16.31        17.75        37.68        24.99        35.61 
TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 TCGA-XE-A8H5 
       23.90        41.52        29.39        34.88        18.38        40.01 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF TCGA-XY-A9T9 
        0.46        55.92        12.07        67.66        41.69         9.24 
TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA0D 
       64.57        31.92        36.59        28.47        37.02        27.88 
TCGA-ZM-AA0F TCGA-ZM-AA0H 
       22.39        57.07 

$subtype2
TCGA-2G-AAG0 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAFI TCGA-2G-AAFL 
       50.27       128.58       203.28        45.21        22.19        24.66 
TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG7 TCGA-2G-AAG8 
       16.54        25.41        22.52        36.13        81.37        75.25 
TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK 
       80.19        84.99        81.47        89.88        96.59       119.05 
TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAH3 
      120.20       132.36       158.33       161.06       172.04        59.90 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-4K-AA1G TCGA-S6-A8JW TCGA-S6-A8JY TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8A9 
       14.33        22.95         9.14        17.23        37.18        36.79 
TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-X3-A8G4 TCGA-XE-A8H1 
       33.07        24.26        24.76        25.45        28.14         6.87 
TCGA-XE-A9SE TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOL TCGA-XY-A89B 
       23.28        65.98        93.93         7.89         0.43        15.48 
TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y TCGA-ZM-AA06 TCGA-ZM-AA0B 
       22.09        27.72        68.02         0.56        49.25        27.55 
TCGA-ZM-AA0N 
       20.84 

$subtype3
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       52.37        26.04        45.67        44.48        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84       103.13       127.92       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       199.23       204.16       244.50        86.96 
TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
        9.63        10.26         4.90        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     0.43     4.90 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
  35.245   45.210   71.240 
[1] "0.1 - 232.8 (35.2)" "0.4 - 230.9 (45.2)" "4.9 - 244.5 (71.2)"
D7V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1 13      11       14        5        0         1         0         1
  subtype2 18       6        9        6        3         4         1         0
  subtype3 15       1        3        0        1         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          1          2
  subtype2         1          1          3          1
  subtype3         1          0          2          2
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  IS               13       18       15
  STAGE I          11        6        1
  STAGE IA         14        9        3
  STAGE IB          5        6        0
  STAGE II          0        3        1
  STAGE IIA         1        4        1
  STAGE IIB         0        1        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        1        2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 31 17  1
  subtype2 25 28  2
  subtype3 20  6  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       31       25       20
  T2       17       28        6
  T3        1        2        3
[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"
          vv
clus       N0 N1+N2
  subtype1 16     2
  subtype2 20     9
  subtype3 10     2
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          16       20       10
  N1+N2        2        9        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 43  0
  subtype2 51  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    0
  subtype2   51    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       43       51       21
  1        0        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 33 16
  subtype2 49  5
  subtype3 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   16
  subtype2   49    5
  subtype3   29    0
     clus
vv    subtype1 subtype2 subtype3
  NO        33       49       29
  YES       16        5        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         2    43
  subtype2     1                         3    51
  subtype3     1                         1    25
D7V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        1
  BLACK OR AFRICAN AMERICAN        2        3        1
  WHITE                           43       51       25
[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"
D7V10, binary
          cls
clus        0  1
  subtype1  4 42
  subtype2  4 49
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   42
  subtype2    4   49
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        4
  NOT HISPANIC OR LATINO       42       49       20
[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 68  1
  subtype2 34  2
  subtype3 28  1
subtype1 subtype2 subtype3 
      69       36       29 
subtype1 subtype2 subtype3 
       1        2        1 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
      154.59        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 
      114.77       128.58       203.28        45.21        73.45       180.07 
TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90        73.91       110.10       182.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      211.89       186.31        17.82        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA 
       13.58         1.38        16.31        17.75        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       24.99        35.61        23.90        41.52        24.76        29.39 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ 
       34.88        25.45        18.38        40.01        23.28        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAO6 TCGA-XE-AAOD 
        0.46        55.92        93.93        12.07         7.89        67.66 
TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S 
       41.69         0.43        15.48         9.24        64.57        31.92 
TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D 
       36.59        28.47        37.02        49.25        27.55        27.88 
TCGA-ZM-AA0F TCGA-ZM-AA0H TCGA-ZM-AA0N 
       22.39        57.07        20.84 

$subtype2
TCGA-2G-AAG0 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       50.27        22.19        24.66        16.54        25.41        22.52 
TCGA-2G-AAFY TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGC TCGA-2G-AAGE 
       36.13        81.37        75.25        80.19        84.99        81.47 
TCGA-2G-AAGF TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGS 
       89.88        96.59       119.05       120.20       132.36       158.33 
TCGA-2G-AAGW TCGA-2G-AAGZ TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL 
      161.06       172.04       208.44       216.92       225.60       230.89 
TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 
      229.22       131.21        17.23        37.18        33.07        24.26 
TCGA-X3-A8G4 TCGA-XE-A8H1 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P TCGA-YU-A90Y 
       28.14         6.87        22.09        27.72        68.02         0.56 

$subtype3
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       52.37        26.04        45.67        44.48        75.58        73.35 
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGT TCGA-2G-AAGV 
       85.84       103.13       127.92       132.10       144.85       148.83 
TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 TCGA-2G-AAL5 TCGA-2G-AALP 
      181.28       175.20       199.23       204.16       244.50        86.96 
TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-XE-AANI TCGA-XE-AAOB TCGA-XE-AAOC 
        9.63        10.26         4.90        34.22        16.87         8.88 
TCGA-XE-AAOJ TCGA-YU-A94D TCGA-YU-A94I TCGA-YU-AA4L TCGA-YU-AA61 
       50.96        71.24        17.62        51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     0.56     4.90 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
   31.92    77.72    71.24 
[1] "0.1 - 232.8 (31.9)" "0.6 - 230.9 (77.7)" "4.9 - 244.5 (71.2)"
D8V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1 18      15       20        7        0         1         1         1
  subtype2 13       2        3        4        3         4         0         0
  subtype3 15       1        3        0        1         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          1          2
  subtype2         1          1          3          1
  subtype3         1          0          2          2
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  IS               18       13       15
  STAGE I          15        2        1
  STAGE IA         20        3        3
  STAGE IB          7        4        0
  STAGE II          0        3        1
  STAGE IIA         1        4        1
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        1        2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 43 23  2
  subtype2 13 22  1
  subtype3 20  6  3
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       13       20
  T2       23       22        6
  T3        2        1        3
[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"
          vv
clus       N0 N1+N2
  subtype1 20     3
  subtype2 16     8
  subtype3 10     2
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          20       16       10
  N1+N2        3        8        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 61  0
  subtype2 33  1
  subtype3 21  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61    0
  subtype2   33    1
  subtype3   21    3
   clus
vv  subtype1 subtype2 subtype3
  0       61       33       21
  1        0        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 46 21
  subtype2 36  0
  subtype3 29  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   21
  subtype2   36    0
  subtype3   29    0
     clus
vv    subtype1 subtype2 subtype3
  NO        46       36       29
  YES       21        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    60
  subtype2     0                         2    34
  subtype3     1                         1    25
D8V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        2        1
  WHITE                           60       34       25
[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"
D8V10, binary
          cls
clus        0  1
  subtype1  6 59
  subtype2  2 32
  subtype3  4 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   59
  subtype2    2   32
  subtype3    4   20
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        4
  NOT HISPANIC OR LATINO       59       32       20
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 67  1
  subtype2 33  1
  subtype3 30  2
subtype1 subtype2 subtype3 
      68       34       32 
subtype1 subtype2 subtype3 
       1        1        2 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAEX TCGA-2G-AAF1 TCGA-2G-AAF4 
      154.59        26.66        20.32        41.39        46.13        76.11 
TCGA-2G-AAF6 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 TCGA-2G-AAH0 
      114.77       128.58       203.28        45.21        73.45       180.07 
TCGA-2G-AAH3 TCGA-2G-AAH8 TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHG TCGA-2G-AAHL 
       59.90        73.91       110.10       182.10        59.80       232.80 
TCGA-2G-AAHN TCGA-2G-AAHP TCGA-2G-AAHT TCGA-2X-A9D5 TCGA-2X-A9D6 TCGA-4K-AA1G 
      211.89       186.31        17.82        14.30        19.96        14.33 
TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-S6-A8JW TCGA-S6-A8JX TCGA-S6-A8JY 
       17.03         0.10        15.88        22.95        18.15         9.14 
TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP TCGA-VF-A8A9 TCGA-VF-A8AA 
       13.58         1.38        16.31        17.75        36.79        37.68 
TCGA-VF-A8AB TCGA-VF-A8AC TCGA-VF-A8AE TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A7V4 
       24.99        35.61        23.90        41.52        24.76        29.39 
TCGA-WZ-A7V5 TCGA-WZ-A8D5 TCGA-XE-A8H4 TCGA-XE-A8H5 TCGA-XE-A9SE TCGA-XE-AANJ 
       34.88        25.45        18.38        40.01        23.28        65.98 
TCGA-XE-AANR TCGA-XE-AANV TCGA-XE-AAO3 TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XE-AAOF 
        0.46        55.92        93.93        12.07        67.66        41.69 
TCGA-XE-AAOL TCGA-XY-A89B TCGA-XY-A9T9 TCGA-YU-A90Q TCGA-YU-A90S TCGA-YU-A90W 
        0.43        15.48         9.24        64.57        31.92        36.59 
TCGA-YU-A912 TCGA-ZM-AA05 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0D TCGA-ZM-AA0F 
       28.47        37.02        49.25        27.55        27.88        22.39 
TCGA-ZM-AA0H TCGA-ZM-AA0N 
       57.07        20.84 

$subtype2
TCGA-2G-AAG0 TCGA-2G-AAFI TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFN TCGA-2G-AAFO 
       50.27        22.19        24.66        16.54        25.41        22.52 
TCGA-2G-AAFY TCGA-2G-AAG7 TCGA-2G-AAG8 TCGA-2G-AAGA TCGA-2G-AAGE TCGA-2G-AAGF 
       36.13        81.37        75.25        80.19        81.47        89.88 
TCGA-2G-AAGJ TCGA-2G-AAGK TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGW TCGA-2G-AAGZ 
       96.59       119.05       120.20       132.36       161.06       172.04 
TCGA-2G-AAKD TCGA-2G-AAKG TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 
      208.44       216.92       225.60       230.89       229.22       131.21 
TCGA-2G-AALP TCGA-SN-A84Y TCGA-VF-A8A8 TCGA-VF-A8AD TCGA-W4-A7U4 TCGA-XE-A8H1 
       86.96        17.23        37.18        33.07        24.26         6.87 
TCGA-XE-AAO6 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90P 
        7.89        22.09        27.72        68.02 

$subtype3
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       52.37        26.04        45.67        44.48        75.58        73.35 
TCGA-2G-AAGC TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGM TCGA-2G-AAGP TCGA-2G-AAGS 
       84.99        85.84       103.13       127.92       132.10       158.33 
TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH2 TCGA-2G-AAH4 
      144.85       148.83       181.28       175.20       199.23       204.16 
TCGA-2G-AAL5 TCGA-SN-A84W TCGA-SN-A84X TCGA-W4-A7U3 TCGA-X3-A8G4 TCGA-XE-AANI 
      244.50         9.63        10.26         4.90        28.14        34.22 
TCGA-XE-AAOB TCGA-XE-AAOC TCGA-XE-AAOJ TCGA-YU-A90Y TCGA-YU-A94D TCGA-YU-A94I 
       16.87         8.88        50.96         0.56        71.24        17.62 
TCGA-YU-AA4L TCGA-YU-AA61 
       51.72        28.41 

subtype1 subtype2 subtype3 
    0.10     6.87     0.56 
subtype1 subtype2 subtype3 
  232.80   230.89   244.50 
subtype1 subtype2 subtype3 
  33.400   77.720   61.805 
[1] "0.1 - 232.8 (33.4)" "6.9 - 230.9 (77.7)" "0.6 - 244.5 (61.8)"
D9V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1 18      15       19        7        0         1         1         1
  subtype2 11       2        4        4        3         4         0         0
  subtype3 17       1        3        0        1         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          1          2
  subtype2         1          1          3          0
  subtype3         1          0          2          3
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  IS               18       11       17
  STAGE I          15        2        1
  STAGE IA         19        4        3
  STAGE IB          7        4        0
  STAGE II          0        3        1
  STAGE IIA         1        4        1
  STAGE IIB         1        0        0
  STAGE IIC         1        0        0
  STAGE III         0        1        1
  STAGE IIIA        0        1        0
  STAGE IIIB        1        3        2
  STAGE IIIC        2        0        3
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 42 23  2
  subtype2 12 22  0
  subtype3 22  6  4
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       42       12       22
  T2       23       22        6
  T3        2        0        4
[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"
          vv
clus       N0 N1+N2
  subtype1 20     3
  subtype2 14     7
  subtype3 12     3
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          20       14       12
  N1+N2        3        7        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 60  0
  subtype2 31  2
  subtype3 24  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    0
  subtype2   31    2
  subtype3   24    2
   clus
vv  subtype1 subtype2 subtype3
  0       60       31       24
  1        0        2        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 46 20
  subtype2 33  1
  subtype3 32  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   20
  subtype2   33    1
  subtype3   32    0
     clus
vv    subtype1 subtype2 subtype3
  NO        46       33       32
  YES       20        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         3    59
  subtype2     0                         1    33
  subtype3     1                         2    27
D9V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        0        1
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           59       33       27
[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"
D9V10, binary
          cls
clus        0  1
  subtype1  6 58
  subtype2  2 31
  subtype3  4 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   58
  subtype2    2   31
  subtype3    4   22
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        4
  NOT HISPANIC OR LATINO       58       31       22
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 32  1
  subtype2 36  0
  subtype3 16  1
  subtype4 19  0
  subtype5 18  1
  subtype6  9  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      33       36       17       19       19       10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        0        1        0        1        1 
$subtype1
TCGA-2G-AAFE TCGA-ZM-AA0E TCGA-2G-AAEW TCGA-2G-AAF1 TCGA-2G-AAF6 TCGA-2G-AAH3 
      154.59        26.66        20.32        46.13       114.77        59.90 
TCGA-2G-AAHA TCGA-2G-AAHC TCGA-2G-AAHL TCGA-2G-AAHN TCGA-2G-AAHT TCGA-2X-A9D6 
      110.10       182.10       232.80       211.89        17.82        19.96 
TCGA-4K-AA1G TCGA-4K-AA1H TCGA-4K-AA1I TCGA-4K-AAAL TCGA-VF-A8AA TCGA-VF-A8AB 
       14.33        17.03         0.10        15.88        37.68        24.99 
TCGA-VF-A8AC TCGA-VF-A8AE TCGA-WZ-A7V4 TCGA-WZ-A7V5 TCGA-XE-A8H4 TCGA-XE-AANR 
       35.61        23.90        29.39        34.88        18.38         0.46 
TCGA-XE-AANV TCGA-XE-AAO4 TCGA-XE-AAOD TCGA-XY-A89B TCGA-YU-A90S TCGA-ZM-AA05 
       55.92        12.07        67.66        15.48        31.92        37.02 
TCGA-ZM-AA0D TCGA-ZM-AA0F TCGA-ZM-AA0H 
       27.88        22.39        57.07 

$subtype2
TCGA-2G-AAEX TCGA-2G-AAF4 TCGA-2G-AAF8 TCGA-2G-AAFG TCGA-2G-AAFH TCGA-2G-AAG9 
       41.39        76.11       128.58       203.28        45.21        73.45 
TCGA-2G-AAH0 TCGA-2G-AAH8 TCGA-2G-AAHG TCGA-2G-AAHP TCGA-2X-A9D5 TCGA-S6-A8JW 
      180.07        73.91        59.80       186.31        14.30        22.95 
TCGA-S6-A8JX TCGA-S6-A8JY TCGA-SB-A6J6 TCGA-SB-A76C TCGA-SN-A6IS TCGA-SO-A8JP 
       18.15         9.14        13.58         1.38        16.31        17.75 
TCGA-VF-A8A9 TCGA-W4-A7U2 TCGA-WZ-A7V3 TCGA-WZ-A8D5 TCGA-XE-A8H5 TCGA-XE-A9SE 
       36.79        41.52        24.76        25.45        40.01        23.28 
TCGA-XE-AANJ TCGA-XE-AAO3 TCGA-XE-AAO6 TCGA-XE-AAOF TCGA-XE-AAOL TCGA-XY-A9T9 
       65.98        93.93         7.89        41.69         0.43         9.24 
TCGA-YU-A90Q TCGA-YU-A90W TCGA-YU-A912 TCGA-ZM-AA06 TCGA-ZM-AA0B TCGA-ZM-AA0N 
       64.57        36.59        28.47        49.25        27.55        20.84 

$subtype3
TCGA-2G-AAFI TCGA-2G-AAFN TCGA-2G-AAG7 TCGA-2G-AAGC TCGA-2G-AAGE TCGA-2G-AAGF 
       22.19        25.41        81.37        84.99        81.47        89.88 
TCGA-2G-AAGK TCGA-2G-AAGS TCGA-2G-AAGW TCGA-2G-AAKG TCGA-2G-AALP TCGA-SN-A84Y 
      119.05       158.33       161.06       216.92        86.96        17.23 
TCGA-VF-A8A8 TCGA-W4-A7U4 TCGA-XY-A8S2 TCGA-XY-A8S3 TCGA-YU-A90Y 
       37.18        24.26        22.09        27.72         0.56 

$subtype4
TCGA-2G-AAG3 TCGA-2G-AAFJ TCGA-2G-AAFV TCGA-2G-AAFZ TCGA-2G-AAG5 TCGA-2G-AAG6 
       52.37        26.04        45.67        44.48        75.58        73.35 
TCGA-2G-AAGM TCGA-2G-AAGT TCGA-2G-AAGV TCGA-2G-AAGX TCGA-2G-AAGY TCGA-2G-AAH4 
      127.92       144.85       148.83       181.28       175.20       204.16 
TCGA-2G-AAL5 TCGA-SN-A84W TCGA-SN-A84X TCGA-XE-AANI TCGA-XE-AAOC TCGA-YU-A94D 
      244.50         9.63        10.26        34.22         8.88        71.24 
TCGA-YU-A94I 
       17.62 

$subtype5
TCGA-2G-AAG0 TCGA-2G-AAFL TCGA-2G-AAFM TCGA-2G-AAFO TCGA-2G-AAFY TCGA-2G-AAG8 
       50.27        24.66        16.54        22.52        36.13        75.25 
TCGA-2G-AAGA TCGA-2G-AAGJ TCGA-2G-AAGN TCGA-2G-AAGO TCGA-2G-AAGZ TCGA-2G-AAKD 
       80.19        96.59       120.20       132.36       172.04       208.44 
TCGA-2G-AAKH TCGA-2G-AAKL TCGA-2G-AAKM TCGA-2G-AAL7 TCGA-VF-A8AD TCGA-XE-A8H1 
      225.60       230.89       229.22       131.21        33.07         6.87 
TCGA-YU-A90P 
       68.02 

$subtype6
TCGA-2G-AAGG TCGA-2G-AAGI TCGA-2G-AAGP TCGA-2G-AAH2 TCGA-W4-A7U3 TCGA-X3-A8G4 
       85.84       103.13       132.10       199.23         4.90        28.14 
TCGA-XE-AAOB TCGA-XE-AAOJ TCGA-YU-AA4L TCGA-YU-AA61 
       16.87        50.96        51.72        28.41 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.10     0.43     0.56     8.88     6.87     4.90 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  232.80   203.28   216.92   244.50   230.89   199.23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   29.39    36.69    81.37    71.24    80.19    51.34 
[1] "0.1 - 232.8 (29.4)" "0.4 - 203.3 (36.7)" "0.6 - 216.9 (81.4)"
[4] "8.9 - 244.5 (71.2)" "6.9 - 230.9 (80.2)" "4.9 - 199.2 (51.3)"
D10V2, continuous
          vv
clus       IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC
  subtype1  8       8       12        3        0         1         0         1
  subtype2 10       7        8        4        0         0         1         0
  subtype3  8       2        1        1        0         0         0         0
  subtype4 10       1        3        0        1         0         0         0
  subtype5  4       0        2        3        3         4         0         0
  subtype6  6       0        0        0        0         1         0         0
          vv
clus       STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0          0          0          0
  subtype2         0          0          1          2
  subtype3         0          0          3          1
  subtype4         1          0          1          0
  subtype5         1          1          1          0
  subtype6         0          0          0          2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  IS                8       10        8       10        4        6
  STAGE I           8        7        2        1        0        0
  STAGE IA         12        8        1        3        2        0
  STAGE IB          3        4        1        0        3        0
  STAGE II          0        0        0        1        3        0
  STAGE IIA         1        0        0        0        4        1
  STAGE IIB         0        1        0        0        0        0
  STAGE IIC         1        0        0        0        0        0
  STAGE III         0        0        0        1        1        0
  STAGE IIIA        0        0        0        0        1        0
  STAGE IIIB        0        1        3        1        1        0
  STAGE IIIC        0        2        1        0        0        2
[1] 12  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1 18 13  1
  subtype2 25 10  1
  subtype3  8  8  1
  subtype4 12  5  2
  subtype5  5 14  0
  subtype6  8  1  1
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       18       25        8       12        5        8
  T2       13       10        8        5       14        1
  T3        1        1        1        2        0        1
[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"
          vv
clus       N0 N1+N2
  subtype1 12     1
  subtype2  8     2
  subtype3  9     2
  subtype4  8     0
  subtype5  6     6
  subtype6  3     2
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          12        8        9        8        6        3
  N1+N2        1        2        2        0        6        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 30  0
  subtype2 31  0
  subtype3 15  1
  subtype4 16  1
  subtype5 17  1
  subtype6  6  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    0
  subtype2   31    0
  subtype3   15    1
  subtype4   16    1
  subtype5   17    1
  subtype6    6    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       30       31       15       16       17        6
  1        0        0        1        1        1        1
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 24  8
  subtype2 22 13
  subtype3 17  0
  subtype4 19  0
  subtype5 19  0
  subtype6 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    8
  subtype2   22   13
  subtype3   17    0
  subtype4   19    0
  subtype5   19    0
  subtype6   10    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        24       22       17       19       19       10
  YES        8       13        0        0        0        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    30
  subtype2     2                         2    30
  subtype3     0                         1    16
  subtype4     1                         0    16
  subtype5     0                         1    18
  subtype6     0                         1     9
D10V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        2        0        1        0
  BLACK OR AFRICAN AMERICAN        1        2        1        0        1
  WHITE                           30       30       16       16       18
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        1
  WHITE                            9
[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"
D10V10, binary
          cls
clus        0  1
  subtype1  2 30
  subtype2  4 29
  subtype3  1 15
  subtype4  3 14
  subtype5  1 17
  subtype6  1  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   30
  subtype2    4   29
  subtype3    1   15
  subtype4    3   14
  subtype5    1   17
  subtype6    1    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            2        4        1        3        1        1
  NOT HISPANIC OR LATINO       30       29       15       14       17        6
[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"
