[1] "ofn"        "-oTESCA-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/ESCA-TP/15078602/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/15092862/ESCA-TP.mergedcluster.txt"

nPatients in clinical file=174, in cluster file=185, common to both=174
[1]  10 174
[1] "CN_CNMF"
[1] 3
 1  2  3 
64 43 66 
 1  2  3 
64 43 66 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
76 31 67 
 1  2  3 
76 31 67 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5  6  7 
24 14 15 21 15 22  5 
 1  2  3  4  5  6  7 
24 14 15 21 15 22  5 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
23 19 20 23 31 
 1  2  3  4  5 
23 19 20 23 31 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
84 65 25 
 1  2  3 
84 65 25 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
67 20 87 
 1  2  3 
67 20 87 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
84 78 11 
 1  2  3 
84 78 11 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
62 26 54 31 
 1  2  3  4 
62 26 54 31 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
66 58 33 11 
 1  2  3  4 
66 58 33 11 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
62 22 84 
 1  2  3 
62 22 84 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATIONS_RADIATION_REGIMENINDICATION"
[12] "NUMBER_PACK_YEARS_SMOKED"              
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 174 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=70,	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=105,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              12-3-2015 26-3-2015
freq.values   "1"       "173"    
freq.contrast "173"     "1"      
both >= 3     "FALSE"   "FALSE"  
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 174 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"           "NEOPLASM_DISEASESTAGE"   
[3] "PATHOLOGY_T_STAGE"        "PATHOLOGY_N_STAGE"       
[5] "PATHOLOGY_M_STAGE"        "GENDER"                  
[7] "NUMBER_PACK_YEARS_SMOKED" "RACE"                    
[9] "ETHNICITY"               
YEARS_TO_BIRTH, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
 1 30 36 86  5 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   31    36    86     5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T0 T1 T2 T3 T4 
 1 30 36 86  5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   31    36    86     5 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
71 65 12  8 
[1] "table(vv)"
vv
N0 N1 N2 N3 
71 65 12  8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
71 65 12  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
71 65 12  8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=45, 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 30 34
  subtype2 30 12
  subtype3 40 25
subtype1 subtype2 subtype3 
      64       42       65 
subtype1 subtype2 subtype3 
      34       12       25 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A4QS 
       13.94         8.94         4.21        32.45        20.09         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43M TCGA-L5-A4OE 
      122.10        60.39        42.77        23.18         8.94        24.00 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       32.61        18.35         7.17         1.38         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE 
        7.13         7.43         2.60         0.36         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN 
        2.66        35.97        12.92        13.48        16.47         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
        8.71        13.41        27.12        46.09        10.36        10.45 
TCGA-LN-A49U TCGA-LN-A49V TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       15.35         0.10        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
       14.70        29.59         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69         7.00        20.02         5.29         4.80 
TCGA-V5-AASW TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-ZR-A9CJ 
        9.27        42.87        46.19        19.73 

$subtype2
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FD 
       16.24         7.69         6.21         9.30        14.86        68.02 
TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        25.41        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        6.28         3.16        30.25         3.68         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
       21.01         3.32        58.59        29.00         8.71        25.12 
TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
        3.02        13.55        13.22         7.76        21.37        83.24 
TCGA-LN-A49X TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-V5-AASV TCGA-V5-AASX 
        0.10         7.82         7.04         9.30        15.35         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       19.96        22.82         1.55        10.16         3.42         2.66 

$subtype3
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-L5-A43H 
        4.67        14.50        12.16        44.75         3.68         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NV TCGA-LN-A49K 
        4.31        47.93         6.94         7.40        52.57         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        13.15        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO 
       13.18         0.13         5.16        20.38         3.42        18.81 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         2.10 

subtype1 subtype2 subtype3 
     0.1      0.1      0.1 
subtype1 subtype2 subtype3 
  122.10    83.24    52.57 
subtype1 subtype2 subtype3 
  12.805   13.385   12.460 
[1] "0.1 - 122.1 (12.8)" "0.1 - 83.2 (13.4)"  "0.1 - 52.6 (12.5)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       4        2        3        0         5        11        12
  subtype2       4        2        1        0        11         9         3
  subtype3       0        1        3        1        23         9        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          3          2        2         2
  subtype2          2          2          3        0         1
  subtype3          7          5          2        3         1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           4        4        0
  STAGE IA          2        2        1
  STAGE IB          3        1        3
  STAGE II          0        0        1
  STAGE IIA         5       11       23
  STAGE IIB        11        9        9
  STAGE III        12        3       10
  STAGE IIIA        3        2        7
  STAGE IIIB        3        2        5
  STAGE IIIC        2        3        2
  STAGE IV          2        0        3
  STAGE IVA         2        1        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    16  7 30  0
  subtype2    10  8 20  1
  subtype3     5 21 35  4
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       16       10        5
  T2           7        8       21
  T3          30       20       35
  T4           0        1        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 18 28  5  2
  subtype2 21 12  2  3
  subtype3 32 24  5  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18       21       32
  N1       28       12       24
  N2        5        2        5
  N3        2        3        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 37  4
  subtype2 32  1
  subtype3 57  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    4
  subtype2   32    1
  subtype3   57    4
   clus
vv  subtype1 subtype2 subtype3
  0       37       32       57
  1        4        1        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  6 58
  subtype2 10 33
  subtype3  8 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   58
  subtype2   10   33
  subtype3    8   58
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        6       10        8
  MALE         58       33       58
[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"
D1V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         0    45
  subtype2     3                         1    38
  subtype3    34                         1    28
D1V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        3       34
  BLACK OR AFRICAN AMERICAN        0        1        1
  WHITE                           45       38       28
[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"
D1V10, binary
          cls
clus        0  1
  subtype1  2 21
  subtype2  1 14
  subtype3  0 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   21
  subtype2    1   14
  subtype3    0   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       21       14       46
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 39 37
  subtype2 20 10
  subtype3 41 25
subtype1 subtype2 subtype3 
      76       30       66 
subtype1 subtype2 subtype3 
      37       10       25 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        5.92        13.94         8.94        32.45         7.69         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
      122.10        60.39        42.77        25.41        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       25.22         3.16        30.25        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        18.35         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y 
        4.90        29.00         7.13         7.43         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       13.41        27.12        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29         4.80         9.27         4.44 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
       22.82        46.19        10.16        19.73 

$subtype2
TCGA-2H-A9GO TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 
       16.24        20.78        20.12        18.64         9.30         0.79 
TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43M 
       23.41        14.86        14.50        21.70         6.28         8.94 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A8NQ 
        3.32         1.38        58.59         6.94         8.71        21.37 
TCGA-L5-A8NU TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A7HY 
       83.24        13.25         0.10        12.76        22.39        12.03 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-AAPN 
        7.04        53.95         1.55        42.87         3.42         2.66 

$subtype3
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        4.21         6.21        33.27        20.09         0.85         2.63 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I 
        0.53        17.03        12.82         9.96         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A43H 
       44.75        68.02         3.68        41.52        24.03         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-LN-A49K 
        4.31        47.93        25.12         7.40        13.55         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       15.35         0.10        12.46        12.59        12.49        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
        0.13         5.16        20.38         3.42        15.35        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.18        15.06        11.24         9.17        15.91         2.10 

subtype1 subtype2 subtype3 
    0.36     0.10     0.10 
subtype1 subtype2 subtype3 
  122.10    83.24    68.02 
subtype1 subtype2 subtype3 
  13.070   13.005   12.445 
[1] "0.4 - 122.1 (13.1)" "0.1 - 83.2 (13.0)"  "0.1 - 68.0 (12.4)" 
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       8        2        3        0         4        14        14
  subtype2       0        1        2        0         9         6         3
  subtype3       0        2        2        1        26         9         9
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          4          4        2         2
  subtype2          5          0          1        0         1
  subtype3          5          6          2        3         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        0        0
  STAGE IA          2        1        2
  STAGE IB          3        2        2
  STAGE II          0        0        1
  STAGE IIA         4        9       26
  STAGE IIB        14        6        9
  STAGE III        14        3        9
  STAGE IIIA        2        5        5
  STAGE IIIB        4        0        6
  STAGE IIIC        4        1        2
  STAGE IV          2        0        3
  STAGE IVA         2        1        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    23  7 33  0
  subtype2     2  8 17  2
  subtype3     6 21 36  3
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       23        2        6
  T2           7        8       21
  T3          33       17       36
  T4           0        2        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 21 34  4  4
  subtype2 14 10  2  1
  subtype3 36 21  6  3
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       21       14       36
  N1       34       10       21
  N2        4        2        6
  N3        4        1        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 46  4
  subtype2 24  1
  subtype3 57  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    4
  subtype2   24    1
  subtype3   57    4
   clus
vv  subtype1 subtype2 subtype3
  0       46       24       57
  1        4        1        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  9 67
  subtype2  4 27
  subtype3 11 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   67
  subtype2    4   27
  subtype3   11   56
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        4       11
  MALE         67       27       56
[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"
D2V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    61
  subtype2     7                         0    22
  subtype3    33                         2    28
D2V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        7       33
  BLACK OR AFRICAN AMERICAN        0        0        2
  WHITE                           61       22       28
[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"
D2V10, binary
          cls
clus        0  1
  subtype1  3 20
  subtype2  0 18
  subtype3  0 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   20
  subtype2    0   18
  subtype3    0   43
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       20       18       43
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 12 12
  subtype2 11  3
  subtype3  9  6
  subtype4 14  6
  subtype5 12  3
  subtype6 13  8
  subtype7  3  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      24       14       15       20       15       21        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      12        3        6        6        3        8        2 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GR TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-JY-A939 TCGA-L5-A43C 
       25.78        32.45         7.69       122.10        21.70         3.16 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        8.94        24.00        32.61        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A8NF 
        7.17         1.38         3.16         7.13         7.43         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-S8-A6BV TCGA-VR-AA4D 
       13.48        16.47        46.09        10.36        20.02        46.19 

$subtype2
TCGA-2H-A9GI TCGA-IG-A97H TCGA-JY-A6FB TCGA-L5-A4OG TCGA-L5-A4OS TCGA-L5-A8NE 
       14.30        14.50        60.39         4.70        58.59        55.50 
TCGA-L5-A8NQ TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-VR-A8EQ 
       21.37        12.49         0.10        12.23        33.11        22.82 
TCGA-Z6-A8JD TCGA-Z6-AAPN 
        3.42         2.66 

$subtype3
TCGA-2H-A9GL TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
        5.92        20.12         9.30         0.53        12.82         9.96 
TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A891 TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A8 
       24.03         0.30         3.95         0.10        12.76        15.52 
TCGA-RE-A7BO TCGA-VR-A8EO TCGA-X8-AAAR 
        7.00        18.81        10.16 

$subtype4
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-JY-A6FA 
        4.21        20.09         2.63         3.88         4.67        44.75 
TCGA-L5-A43E TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49R 
       30.25        13.55        13.22         5.92        10.45         0.10 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO 
        0.10        12.46        25.25        12.00        13.18         0.13 
TCGA-S8-A6BW TCGA-Z6-A8JE 
       20.38         2.10 

$subtype5
TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-JY-A93E TCGA-L5-A4OF 
        6.21        20.78        18.64        23.41        25.22         3.68 
TCGA-L5-A4OT TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49W TCGA-LN-A4MQ 
        4.90        13.41        27.12        52.57        13.25        12.33 
TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-VR-AA7B 
       12.03         7.82        11.24 

$subtype6
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A97I TCGA-JY-A6FD 
       33.27         0.85        17.03         0.79        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-L5-A43J TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
        3.68        41.52         4.31        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR 
       15.35        12.59        12.59        22.39        11.54        13.22 
TCGA-LN-A5U6 TCGA-Q9-A6FU TCGA-VR-A8Q7 
       12.33         5.16        42.87 

$subtype7
TCGA-L5-A4OU TCGA-L5-A88W TCGA-LN-A49S TCGA-LN-A5U5 TCGA-VR-A8EP 
       29.00        25.12        13.15         4.47        19.96 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1.38     0.10     0.10     0.10     3.68     0.79     4.47 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  122.10    60.39    24.03    44.75    52.57    68.02    29.00 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  17.410   14.400    9.960   11.225   13.250   12.590   19.960 
[1] "1.4 - 122.1 (17.4)" "0.1 - 60.4 (14.4)"  "0.1 - 24.0 (10.0)" 
[4] "0.1 - 44.8 (11.2)"  "3.7 - 52.6 (13.2)"  "0.8 - 68.0 (12.6)" 
[7] "4.5 - 29.0 (20.0)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        2        2        0         1         5         3
  subtype2       2        0        0        1         6         3         2
  subtype3       0        0        1        0         3         2         3
  subtype4       1        0        1        0        10         2         3
  subtype5       0        1        0        0         1         5         3
  subtype6       0        0        1        0        10         5         3
  subtype7       0        0        0        0         3         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          1          2        0         1
  subtype2          0          0          0        0         0
  subtype3          2          2          0        0         0
  subtype4          2          2          0        0         0
  subtype5          2          1          0        2         0
  subtype6          2          1          0        0         0
  subtype7          0          1          0        1         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           3        2        0        1        0        0        0
  STAGE IA          2        0        0        0        1        0        0
  STAGE IB          2        0        1        1        0        1        0
  STAGE II          0        1        0        0        0        0        0
  STAGE IIA         1        6        3       10        1       10        3
  STAGE IIB         5        3        2        2        5        5        0
  STAGE III         3        2        3        3        3        3        0
  STAGE IIIA        2        0        2        2        2        2        0
  STAGE IIIB        1        0        2        2        1        1        1
  STAGE IIIC        2        0        0        0        0        0        0
  STAGE IV          0        0        0        0        2        0        1
  STAGE IVA         1        0        0        0        0        0        0
[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       T0+T1 T2 T3 T4
  subtype1    10  4  9  0
  subtype2     2  5  7  0
  subtype3     2  3 10  0
  subtype4     1  7 13  0
  subtype5     2  1 11  1
  subtype6     1  8 12  1
  subtype7     0  0  5  0
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1       10        2        2        1        2        1        0
  T2           4        5        3        7        1        8        0
  T3           9        7       10       13       11       12        5
  T4           0        0        0        0        1        1        0
[1] 4 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 N3
  subtype1  7 11  3  2
  subtype2  9  4  0  0
  subtype3  5  9  1  0
  subtype4 13  6  2  0
  subtype5  6  7  1  1
  subtype6 13  8  1  0
  subtype7  3  1  1  0
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0        7        9        5       13        6       13        3
  N1       11        4        9        6        7        8        1
  N2        3        0        1        2        1        1        1
  N3        2        0        0        0        1        0        0
[1] 4 7
[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 13  1
  subtype2 14  0
  subtype3 14  0
  subtype4 20  0
  subtype5 12  2
  subtype6 21  0
  subtype7  3  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   14    0
  subtype3   14    0
  subtype4   20    0
  subtype5   12    2
  subtype6   21    0
  subtype7    3    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       13       14       14       20       12       21        3
  1        1        0        0        0        2        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"
D3V7, binary
          cls
clus        0  1
  subtype1  4 20
  subtype2  2 12
  subtype3  2 13
  subtype4  1 20
  subtype5  3 12
  subtype6  3 19
  subtype7  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   20
  subtype2    2   12
  subtype3    2   13
  subtype4    1   20
  subtype5    3   12
  subtype6    3   19
  subtype7    0    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        4        2        2        1        3        3        0
  MALE         20       12       13       20       12       19        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"
D3V8, continuous
          vv
clus       ASIAN WHITE
  subtype1     0    20
  subtype2     4     8
  subtype3     5     9
  subtype4    12     8
  subtype5     3    12
  subtype6    12    10
  subtype7     2     3
D3V9, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  ASIAN        0        4        5       12        3       12        2
  WHITE       20        8        9        8       12       10        3
[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"
D3V10, binary
          cls
clus        0
  subtype1  3
  subtype2  6
  subtype3 10
  subtype4 16
  subtype5  7
  subtype6 17
  subtype7  2
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 12 11
  subtype2 14  5
  subtype3 12  8
  subtype4 14  7
  subtype5 22  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      23       19       20       21       31 
subtype1 subtype2 subtype3 subtype4 subtype5 
      11        5        8        7        9 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A939 TCGA-L5-A43C 
       25.78        32.45         7.69         3.88        21.70         3.16 
TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       30.25         8.94        24.00        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A8NI 
       18.35         7.17         1.38         3.16         7.13        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-S8-A6BV TCGA-VR-AA4D 
       16.47        46.09        10.36        20.02        46.19 

$subtype2
TCGA-2H-A9GI TCGA-IG-A3YC TCGA-IG-A50L TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FB 
       14.30        20.12         0.53         9.96       122.10        60.39 
TCGA-JY-A93F TCGA-L5-A4OG TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NQ 
       24.03         4.70        58.59         3.95        55.50        21.37 
TCGA-LN-A4A8 TCGA-M9-A5M8 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-Z6-A8JD 
       15.52        33.11         7.00        18.81        22.82         3.42 
TCGA-Z6-AAPN 
        2.66 

$subtype3
TCGA-2H-A9GL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-JY-A93E 
        5.92        20.78        18.64         9.30        12.82        25.22 
TCGA-L5-A4OF TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A8NF TCGA-L5-A8NS TCGA-L5-A8NT 
        3.68         4.90         7.43         2.66        13.41        27.12 
TCGA-L5-A8NV TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HY TCGA-Q9-A6FW 
       52.57        13.25         0.10        12.76        12.03         7.82 
TCGA-VR-AA7B TCGA-X8-AAAR 
       11.24        10.16 

$subtype4
TCGA-2H-A9GQ TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FE 
        4.21         0.79        23.41         4.67        14.50         3.68 
TCGA-L5-A43H TCGA-L5-A8NL TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        0.30        13.22        12.43        13.41         0.10        15.35 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
        0.10        12.49        12.59        22.39         0.10        11.54 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-VR-A8Q7 
       12.23        13.18        42.87 

$subtype5
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A51D 
        6.21        33.27        20.09         0.85         2.63        17.03 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A43J TCGA-L5-A4OU 
       12.16        44.75        68.02        41.52         4.31        29.00 
TCGA-L5-A88W TCGA-L5-A8NK TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S 
       25.12        13.55         5.92        10.45        12.66        13.15 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.46        12.59        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-VR-A8EP 
       25.25        12.00         0.13         5.16        20.38        19.96 
TCGA-Z6-A8JE 
        2.10 

subtype1 subtype2 subtype3 subtype4 subtype5 
    1.38     0.53     0.10     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   46.19   122.10    52.57    42.87    68.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
  18.350   18.810   11.635   12.430   12.590 
[1] "1.4 - 46.2 (18.4)"  "0.5 - 122.1 (18.8)" "0.1 - 52.6 (11.6)" 
[4] "0.1 - 42.9 (12.4)"  "0.1 - 68.0 (12.6)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        2        2        0         1         4         3
  subtype2       3        0        1        0         4         5         2
  subtype3       0        0        0        0         3         5         4
  subtype4       0        0        1        1        10         3         6
  subtype5       0        1        1        0        16         5         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          2          2        0         0
  subtype2          2          1          0        0         0
  subtype3          2          2          0        2         1
  subtype4          1          1          0        0         0
  subtype5          3          2          0        1         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           3        3        0        0        0
  STAGE IA          2        0        0        0        1
  STAGE IB          2        1        0        1        1
  STAGE II          0        0        0        1        0
  STAGE IIA         1        4        3       10       16
  STAGE IIB         4        5        5        3        5
  STAGE III         3        2        4        6        2
  STAGE IIIA        2        2        2        1        3
  STAGE IIIB        2        1        2        1        2
  STAGE IIIC        2        0        0        0        0
  STAGE IV          0        0        2        0        1
  STAGE IVA         0        0        1        0        0
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     9  3 10  0
  subtype2     4  6  9  0
  subtype3     3  2 14  1
  subtype4     0  7 16  0
  subtype5     2 10 18  1
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        9        4        3        0        2
  T2           3        6        2        7       10
  T3          10        9       14       16       18
  T4           0        0        1        0        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1  6 10  4  2
  subtype2 10  9  0  0
  subtype3  7 10  2  1
  subtype4 12  9  1  0
  subtype5 21  8  2  0
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0        6       10        7       12       21
  N1       10        9       10        9        8
  N2        4        0        2        1        2
  N3        2        0        1        0        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1 13  0
  subtype2 19  0
  subtype3 15  3
  subtype4 23  0
  subtype5 27  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    0
  subtype2   19    0
  subtype3   15    3
  subtype4   23    0
  subtype5   27    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       13       19       15       23       27
  1        0        0        3        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1  4 19
  subtype2  4 15
  subtype3  1 19
  subtype4  1 22
  subtype5  5 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   19
  subtype2    4   15
  subtype3    1   19
  subtype4    1   22
  subtype5    5   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        4        4        1        1        5
  MALE         19       15       19       22       26
[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"
D4V8, continuous
          vv
clus       ASIAN WHITE
  subtype1     0    19
  subtype2     2    15
  subtype3     5    14
  subtype4    16     6
  subtype5    15    16
D4V9, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN        0        2        5       16       15
  WHITE       19       15       14        6       16
[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"
D4V10, binary
          cls
clus        0
  subtype1  4
  subtype2  7
  subtype3  9
  subtype4 18
  subtype5 23
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 44 40
  subtype2 41 22
  subtype3 15 10
subtype1 subtype2 subtype3 
      84       63       25 
subtype1 subtype2 subtype3 
      40       22       10 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24        32.45         7.69 
TCGA-IG-A4QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 
        3.88        14.86       122.10        60.39        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        52.57        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69         7.00        20.02         5.29         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
        9.27         4.44        22.82        46.19        10.16        19.73 

$subtype2
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43J 
        4.67        14.50        12.16         3.68         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       47.93         6.94         5.92        10.45        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.00        12.03        13.18         0.13         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY 
        3.42        15.35        18.81        12.43        18.31        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        3.42         2.10         2.66 

$subtype3
TCGA-IC-A6RF TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FA TCGA-JY-A6FD 
        6.21        20.12        18.64         0.79        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       41.52        24.03         6.28         8.71        25.12         7.40 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A4A3 
       13.55        21.37        46.09        12.66        13.15        12.76 
TCGA-LN-A4MR TCGA-LN-A7HX TCGA-R6-A6Y0 TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
       13.22        12.23        53.95        19.96         1.55         8.12 
TCGA-VR-A8EX 
       28.11 

subtype1 subtype2 subtype3 
    0.36     0.10     0.79 
subtype1 subtype2 subtype3 
  122.10    47.93    68.02 
subtype1 subtype2 subtype3 
   13.07    12.33    13.55 
[1] "0.4 - 122.1 (13.1)" "0.1 - 47.9 (12.3)"  "0.8 - 68.0 (13.6)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       8        2        2        0         5        16        14
  subtype2       0        1        2        1        24        10        10
  subtype3       0        2        3        0        10         3         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          4          4          5        2         3
  subtype2          7          4          2        3         0
  subtype3          1          2          0        0         1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        0        0
  STAGE IA          2        1        2
  STAGE IB          2        2        3
  STAGE II          0        1        0
  STAGE IIA         5       24       10
  STAGE IIB        16       10        3
  STAGE III        14       10        2
  STAGE IIIA        4        7        1
  STAGE IIIB        4        4        2
  STAGE IIIC        5        2        0
  STAGE IV          2        3        0
  STAGE IVA         3        0        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    24  9 36  1
  subtype2     3 17 40  4
  subtype3     4 10 10  0
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       24        3        4
  T2           9       17       10
  T3          36       40       10
  T4           1        4        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 22 36  6  5
  subtype2 36 20  4  3
  subtype3 13  9  2  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       22       36       13
  N1       36       20        9
  N2        6        4        2
  N3        5        3        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 49  5
  subtype2 56  3
  subtype3 22  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    5
  subtype2   56    3
  subtype3   22    1
   clus
vv  subtype1 subtype2 subtype3
  0       49       56       22
  1        5        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"
D5V7, binary
          cls
clus        0  1
  subtype1 12 72
  subtype2  7 58
  subtype3  5 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   72
  subtype2    7   58
  subtype3    5   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12        7        5
  MALE         72       58       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"
D5V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    67
  subtype2    32                         2    28
  subtype3     8                         0    16
D5V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1       32        8
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                           67       28       16
[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"
D5V10, binary
          cls
clus        0  1
  subtype1  3 22
  subtype2  0 48
  subtype3  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   22
  subtype2    0   48
  subtype3    0   11
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       22       48       11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 35 32
  subtype2 11  9
  subtype3 54 31
subtype1 subtype2 subtype3 
      67       20       85 
subtype1 subtype2 subtype3 
      32        9       31 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP 
        5.92         8.94        16.24        32.45         7.69        14.86 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       31.56        25.22         3.16        30.25         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.43         3.95        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.41        27.12        83.24        10.36         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
        5.06        29.59         9.30        15.78         1.45        12.69 
TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        7.00         4.80         9.27         4.44        22.82        46.19 
TCGA-ZR-A9CJ 
       19.73 

$subtype2
TCGA-2H-A9GM TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88V 
       13.94         3.88        24.00         4.70         8.71         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.36         3.02        52.57        46.09        33.11         7.82 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BV 
       14.70         7.04         6.35        53.95         2.89        20.02 
TCGA-V5-A7RB TCGA-X8-AAAR 
        5.29        10.16 

$subtype3
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F 
       12.16        44.75        68.02         3.68        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W 
        6.28         0.30         4.31        47.93         6.94        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.23        12.03        13.18         0.13         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35        18.81        19.96        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

subtype1 subtype2 subtype3 
    1.38     0.36     0.10 
subtype1 subtype2 subtype3 
  122.10    53.95    68.02 
subtype1 subtype2 subtype3 
  13.480    8.265   12.460 
[1] "1.4 - 122.1 (13.5)" "0.4 - 54.0 (8.3)"   "0.1 - 68.0 (12.5)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       6        2        2        0         3        15        13
  subtype2       2        0        1        0         2         2         1
  subtype3       0        3        4        1        34        12        12
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          3          1          5        2         3
  subtype2          1          3          0        0         0
  subtype3          8          6          2        3         1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           6        2        0
  STAGE IA          2        0        3
  STAGE IB          2        1        4
  STAGE II          0        0        1
  STAGE IIA         3        2       34
  STAGE IIB        15        2       12
  STAGE III        13        1       12
  STAGE IIIA        3        1        8
  STAGE IIIB        1        3        6
  STAGE IIIC        5        0        2
  STAGE IV          2        0        3
  STAGE IVA         3        0        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    18  9 29  1
  subtype2     6  2  7  0
  subtype3     7 25 50  4
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       18        6        7
  T2           9        2       25
  T3          29        7       50
  T4           1        0        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 17 31  3  5
  subtype2  5  7  3  0
  subtype3 49 27  6  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17        5       49
  N1       31        7       27
  N2        3        3        6
  N3        5        0        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 42  5
  subtype2  9  0
  subtype3 76  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    5
  subtype2    9    0
  subtype3   76    4
   clus
vv  subtype1 subtype2 subtype3
  0       42        9       76
  1        5        0        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 10 57
  subtype2  2 18
  subtype3 12 75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   57
  subtype2    2   18
  subtype3   12   75
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10        2       12
  MALE         57       18       75
[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"
D6V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    53
  subtype2     0                         0    17
  subtype3    40                         2    41
D6V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0       40
  BLACK OR AFRICAN AMERICAN        0        0        2
  WHITE                           53       17       41
[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"
D6V10, binary
          cls
clus        0  1
  subtype1  2 14
  subtype2  1  9
  subtype3  0 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   14
  subtype2    1    9
  subtype3    0   58
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       14        9       58
[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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 43 41
  subtype2 48 29
  subtype3  8  2
subtype1 subtype2 subtype3 
      84       77       10 
subtype1 subtype2 subtype3 
      41       29        2 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24        32.45         7.69 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
        3.88       122.10        60.39        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OE 
       23.18        31.56         3.16        30.25         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.68         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.13         7.43         2.60         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       27.12        83.24        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69         7.00        20.02         5.29         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ 
        9.27         4.44        22.82        46.19        10.16        19.73 

$subtype2
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC 
        4.21         6.21        33.27        20.09         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W 
        3.68        41.52        24.03         4.31        47.93        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37         5.92        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       13.41         0.10        13.15        15.35        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       13.18         0.13         5.16        20.38         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91         3.42         2.10         2.66 

$subtype3
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A93E TCGA-KH-A6WC 
       20.78         2.63         9.30        14.86        25.22         6.28 
TCGA-L5-A43H TCGA-L5-A88S TCGA-L5-A88T TCGA-LN-A49N 
        0.30         6.94         8.71        12.43 

subtype1 subtype2 subtype3 
    0.36     0.10     0.30 
subtype1 subtype2 subtype3 
  122.10    68.02    25.22 
subtype1 subtype2 subtype3 
  13.070   12.590    9.005 
[1] "0.4 - 122.1 (13.1)" "0.1 - 68.0 (12.6)"  "0.3 - 25.2 (9.0)"  
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       8        2        3        0         5        16        14
  subtype2       0        2        3        1        31        11        11
  subtype3       0        1        1        0         2         2         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          4          5        2         3
  subtype2          6          6          2        3         1
  subtype3          4          0          0        0         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        0        0
  STAGE IA          2        2        1
  STAGE IB          3        3        1
  STAGE II          0        1        0
  STAGE IIA         5       31        2
  STAGE IIB        16       11        2
  STAGE III        14       11        1
  STAGE IIIA        2        6        4
  STAGE IIIB        4        6        0
  STAGE IIIC        5        2        0
  STAGE IV          2        3        0
  STAGE IVA         3        1        0
[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       T0+T1 T2 T3 T4
  subtype1    24 10 35  0
  subtype2     6 24 44  3
  subtype3     1  2  6  2
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       24        6        1
  T2          10       24        2
  T3          35       44        6
  T4           0        3        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 22 36  6  5
  subtype2 43 24  6  3
  subtype3  5  5  0  0
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       22       43        5
  N1       36       24        5
  N2        6        6        0
  N3        5        3        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 49  5
  subtype2 68  4
  subtype3  9  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49    5
  subtype2   68    4
  subtype3    9    0
   clus
vv  subtype1 subtype2 subtype3
  0       49       68        9
  1        5        4        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"
D7V7, binary
          cls
clus        0  1
  subtype1 11 73
  subtype2 12 66
  subtype3  1 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   73
  subtype2   12   66
  subtype3    1   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       11       12        1
  MALE         73       66       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    67
  subtype2    37                         2    35
  subtype3     2                         0     9
D7V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1       37        2
  BLACK OR AFRICAN AMERICAN        0        2        0
  WHITE                           67       35        9
[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  3 22
  subtype2  0 51
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   22
  subtype2    0   51
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       22       51        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 27 35
  subtype2 19  7
  subtype3 31 21
  subtype4 22  9
subtype1 subtype2 subtype3 subtype4 
      62       26       52       31 
subtype1 subtype2 subtype3 subtype4 
      35        7       21        9 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        20.05        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-JY-A6F8 
       13.94         8.94        16.24         4.21         3.88       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF 
       60.39        42.77        23.18        30.25        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        4.70        32.61        19.99        21.01        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        1.38         3.16        58.59         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.95        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       16.47         7.76         5.49        46.09        10.36        33.11 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00         5.29         4.80         9.27         4.44        22.82 
TCGA-VR-AA4D TCGA-ZR-A9CJ 
       46.19        19.73 

$subtype2
TCGA-2H-A9GH TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A7DP TCGA-JY-A938 TCGA-JY-A939 
       31.27        32.45         7.69        14.86        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OO TCGA-L5-A4OT 
       31.56        25.22         3.16         8.94         3.32         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NR 
       29.00         8.71         3.02        35.97        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.41        27.12        83.24        52.57         7.82         7.59 
TCGA-S8-A6BV TCGA-X8-AAAR 
       20.02        10.16 

$subtype3
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
       18.64         9.30         0.53        23.41        12.82         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
       14.50        12.16         3.68         6.28         0.30         4.31 
TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
        6.94         7.40        21.37         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.41         0.10        13.25         0.10        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        22.39         0.10        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.33        12.03        13.18         0.13         5.16        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        3.42        15.35        19.96        12.43         1.55         8.12 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        15.06         9.17        15.91 

$subtype4
TCGA-IG-A3YC TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD 
       20.12        17.03         0.79         4.67        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A8NK TCGA-LN-A49M 
       41.52        24.03        47.93        25.12        13.55        12.66 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.15        15.35        12.46        12.76        15.52        11.54 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-VR-A8EO TCGA-VR-A8EU 
       25.25        10.52        12.00        12.23        18.81        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-A8JE 
       28.11        30.71        42.87        11.24         3.42         2.10 
TCGA-Z6-AAPN 
        2.66 

subtype1 subtype2 subtype3 subtype4 
    0.36     3.02     0.10     0.79 
subtype1 subtype2 subtype3 subtype4 
  122.10    83.24    33.27    68.02 
subtype1 subtype2 subtype3 subtype4 
  11.525   14.135   12.245   15.350 
[1] "0.4 - 122.1 (11.5)" "3.0 - 83.2 (14.1)"  "0.1 - 33.3 (12.2)" 
[4] "0.8 - 68.0 (15.3)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       7        2        3        0         1        10        12
  subtype2       1        0        0        0         4         7         3
  subtype3       0        2        2        1        18         9         9
  subtype4       0        1        2        0        15         3         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          3          3        1         3
  subtype2          3          1          2        1         0
  subtype3          5          4          2        1         0
  subtype4          3          2          0        2         1
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           7        1        0        0
  STAGE IA          2        0        2        1
  STAGE IB          3        0        2        2
  STAGE II          0        0        1        0
  STAGE IIA         1        4       18       15
  STAGE IIB        10        7        9        3
  STAGE III        12        3        9        2
  STAGE IIIA        1        3        5        3
  STAGE IIIB        3        1        4        2
  STAGE IIIC        3        2        2        0
  STAGE IV          1        1        1        2
  STAGE IVA         3        0        0        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       T0+T1 T2 T3 T4
  subtype1    19  8 22  0
  subtype2     5  3 15  1
  subtype3     3 16 30  4
  subtype4     4  9 18  0
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       19        5        3        4
  T2           8        3       16        9
  T3          22       15       30       18
  T4           0        1        4        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 14 28  4  3
  subtype2  8 11  2  2
  subtype3 28 17  5  2
  subtype4 20  9  1  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       14        8       28       20
  N1       28       11       17        9
  N2        4        2        5        1
  N3        3        2        2        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 33  4
  subtype2 19  1
  subtype3 48  1
  subtype4 26  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33    4
  subtype2   19    1
  subtype3   48    1
  subtype4   26    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       33       19       48       26
  1        4        1        1        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1  7 55
  subtype2  5 21
  subtype3  6 48
  subtype4  6 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   55
  subtype2    5   21
  subtype3    6   48
  subtype4    6   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7        5        6        6
  MALE         55       21       48       25
[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"
D8V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    48
  subtype2     0                         0    22
  subtype3    25                         2    25
  subtype4    14                         0    16
D8V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0       25       14
  BLACK OR AFRICAN AMERICAN        0        0        2        0
  WHITE                           48       22       25       16
[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"
D8V10, binary
          cls
clus        0  1
  subtype1  3 17
  subtype2  0  6
  subtype3  0 39
  subtype4  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   17
  subtype2    0    6
  subtype3    0   39
  subtype4    0   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        0        0
  NOT HISPANIC OR LATINO       17        6       39       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 32 34
  subtype2 34 24
  subtype3 23  9
  subtype4  5  5
subtype1 subtype2 subtype3 subtype4 
      66       58       32       10 
subtype1 subtype2 subtype3 subtype4 
      34       24        9        5 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 
        5.92        13.94         8.94        16.24         3.88       122.10 
TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E 
       60.39        42.77        25.41        23.18         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON 
        8.94        24.00         4.70        32.61        19.99        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.13         7.43         2.60         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
       55.50         2.66        12.92        13.48        16.47         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN 
        5.49         8.71        46.09        10.36        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70        29.59         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89        12.69         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
        4.80         9.27         4.44        22.82        46.19        10.16 

$subtype2
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 
        4.21         6.21        20.09        18.64        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41        12.82         9.96         4.67        14.50        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
        3.68        41.52         4.31        47.93        25.12         7.40 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.66        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 
       15.35        12.46        12.59        12.49        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP 
        0.13         5.16        20.38         3.42        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-AAPN 
       42.87        11.24         9.17         2.66 

$subtype3
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45         7.69        33.27        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A939 TCGA-JY-A93D 
        9.30         0.53        14.86        12.16        21.70        31.56 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A88S 
       25.22         6.28         0.30         3.68         3.32         6.94 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
        8.71        35.97        13.55        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 
       83.24        52.57        12.43        13.25         0.10        22.39 
TCGA-Q9-A6FW TCGA-VR-AA7I 
        7.82        15.91 

$subtype4
TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A8NL TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-VR-A8ET 
        0.85        68.02        13.22         7.04         9.30         1.55 
TCGA-VR-AA4G TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.06         3.42         2.10        19.73 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.10     0.10     0.85 
subtype1 subtype2 subtype3 subtype4 
  122.10    47.93    83.24    68.02 
subtype1 subtype2 subtype3 subtype4 
  11.525   12.475   13.480    8.170 
[1] "0.4 - 122.1 (11.5)" "0.1 - 47.9 (12.5)"  "0.1 - 83.2 (13.5)" 
[4] "0.8 - 68.0 (8.2)"  
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       7        2        3        0         2        11        12
  subtype2       0        2        2        1        23         8         8
  subtype3       0        1        1        0        11         7         4
  subtype4       0        0        0        0         2         2         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          2          3          2        2         3
  subtype2          1          6          2        3         1
  subtype3          6          1          2        0         0
  subtype4          3          0          1        0         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           7        0        0        0
  STAGE IA          2        2        1        0
  STAGE IB          3        2        1        0
  STAGE II          0        1        0        0
  STAGE IIA         2       23       11        2
  STAGE IIB        11        8        7        2
  STAGE III        12        8        4        1
  STAGE IIIA        2        1        6        3
  STAGE IIIB        3        6        1        0
  STAGE IIIC        2        2        2        1
  STAGE IV          2        3        0        0
  STAGE IVA         3        1        0        0
[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       T0+T1 T2 T3 T4
  subtype1    20  8 26  0
  subtype2     6 17 33  1
  subtype3     4  7 19  3
  subtype4     0  3  5  1
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       20        6        4        0
  T2           8       17        7        3
  T3          26       33       19        5
  T4           0        1        3        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 16 31  5  2
  subtype2 30 18  5  3
  subtype3 17 12  1  2
  subtype4  4  3  1  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       16       30       17        4
  N1       31       18       12        3
  N2        5        5        1        1
  N3        2        3        2        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 36  5
  subtype2 49  4
  subtype3 30  0
  subtype4  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    5
  subtype2   49    4
  subtype3   30    0
  subtype4    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36       49       30        8
  1        5        4        0        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"
D9V7, binary
          cls
clus        0  1
  subtype1 10 56
  subtype2  7 51
  subtype3  3 30
  subtype4  2  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   56
  subtype2    7   51
  subtype3    3   30
  subtype4    2    9
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       10        7        3        2
  MALE         56       51       30        9
[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"
D9V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    50
  subtype2    30                         1    23
  subtype3     6                         0    26
  subtype4     2                         0     9
D9V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1       30        6        2
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                           50       23       26        9
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus        0  1
  subtype1  2 17
  subtype2  0 39
  subtype3  0 15
  subtype4  1  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   17
  subtype2    0   39
  subtype3    0   15
  subtype4    1    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        0        0        1
  NOT HISPANIC OR LATINO       17       39       15        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 26 36
  subtype2 16  6
  subtype3 52 30
subtype1 subtype2 subtype3 
      62       22       82 
subtype1 subtype2 subtype3 
      36        6       30 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS 
        5.92        13.94         8.94        16.24         4.21         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OE 
      122.10        60.39        42.77        23.18        30.25        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP 
        3.68         4.70        32.61        19.99        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        1.38         3.16        58.59         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.95        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ 
       16.47         7.76         5.49         8.71        46.09        10.36 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         8.02         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00         5.29         4.80         9.27         4.44        22.82 
TCGA-VR-AA4D TCGA-ZR-A9CJ 
       46.19        19.73 

$subtype2
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       32.45         7.69        25.41        21.70        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 
        3.16         8.94         3.32         4.90        29.00         3.02 
TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       35.97        13.22        13.41        27.12        83.24        52.57 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV TCGA-X8-AAAR 
        7.82         7.59        20.02        10.16 

$subtype3
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-KH-A6WC 
       12.16        44.75        68.02         3.68        41.52         6.28 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        0.30         4.31        47.93         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        7.40        13.55        21.37         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO 
       13.18         0.13         5.16        20.38         3.42        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.91         3.42         2.10         2.66 

subtype1 subtype2 subtype3 
    0.36     3.02     0.10 
subtype1 subtype2 subtype3 
  122.10    83.24    68.02 
subtype1 subtype2 subtype3 
  11.525   16.715   12.445 
[1] "0.4 - 122.1 (11.5)" "3.0 - 83.2 (16.7)"  "0.1 - 68.0 (12.4)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       6        2        3        0         1        11        13
  subtype2       1        0        0        0         4         5         2
  subtype3       0        3        3        1        33        12        10
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1          1          3          3        1         3
  subtype2          2          1          2        1         0
  subtype3          9          6          2        3         1
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           6        1        0
  STAGE IA          2        0        3
  STAGE IB          3        0        3
  STAGE II          0        0        1
  STAGE IIA         1        4       33
  STAGE IIB        11        5       12
  STAGE III        13        2       10
  STAGE IIIA        1        2        9
  STAGE IIIB        3        1        6
  STAGE IIIC        3        2        2
  STAGE IV          1        1        3
  STAGE IVA         3        0        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    19  8 23  0
  subtype2     4  2 14  0
  subtype3     7 25 46  5
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19        4        7
  T2           8        2       25
  T3          23       14       46
  T4           0        0        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 13 30  4  3
  subtype2  8  8  2  2
  subtype3 46 26  6  3
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       13        8       46
  N1       30        8       26
  N2        4        2        6
  N3        3        2        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 34  4
  subtype2 16  1
  subtype3 73  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    4
  subtype2   16    1
  subtype3   73    4
   clus
vv  subtype1 subtype2 subtype3
  0       34       16       73
  1        4        1        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1  7 55
  subtype2  3 19
  subtype3 12 72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   55
  subtype2    3   19
  subtype3   12   72
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7        3       12
  MALE         55       19       72
[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"
D10V8, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    46
  subtype2     0                         0    20
  subtype3    38                         1    42
D10V9, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0       38
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                           46       20       42
[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"
D10V10, binary
          cls
clus        0  1
  subtype1  3 16
  subtype2  0  5
  subtype3  0 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   16
  subtype2    0    5
  subtype3    0   56
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        0
  NOT HISPANIC OR LATINO       16        5       56
[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"
