[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTMESO-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/MESO-TP/10006044/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/MESO-TP/10668104/MESO-TP.mergedcluster.txt"

nPatients in clinical file=21, in cluster file=37, common to both=21
[1]  8 21
[1] "CN_CNMF"
[1] 3
 1  2 
 9 12 
 1  2 
 9 12 
[1] "METHLYATION_CNMF"
[1] 3
 1  2 
11 10 
 1  2 
11 10 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
11 10 
 1  2 
11 10 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
11  4  6 
 1  2  3 
11  4  6 
[1] "MIRSEQ_CNMF"
[1] 3
1 2 
9 7 
1 2 
9 7 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 
3 3 4 2 2 1 1 
1 2 3 
3 3 4 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
1 2 
8 8 
1 2 
8 8 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 
2 3 5 2 2 2 
2 3 
3 5 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "KARNOFSKYPERFORMANCESCORE"             
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 21 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
          NA           NA           NA           NA          371           NA 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
          NA           NA         1316         1575          414            7 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 21 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 3 10  7  1 
[1] "table(vv)"
vv
T1+T2 T3+T4 
   13     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 3 10  7  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 13

$Class1_nSamples
[1] 8

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
   13     8 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
14  4  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   14     6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
14  4  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 14

$Class1_nSamples
[1] 6

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   14     6 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2      0 1
  subtype1 2 7
  subtype2 3 9
subtype1 subtype2 
       9       12 
subtype1 subtype2 
       7        9 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       17.95         1.87        12.20        18.81        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-SH-A7BC 
        3.52        13.61        23.90 

$subtype2
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A6BL 
        8.02        31.20        80.84        91.73         5.19        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
       24.89        43.27        51.78         0.23        15.09         7.99 

subtype1 subtype2 
    1.87     0.23 
subtype1 subtype2 
   23.90    91.73 
subtype1 subtype2 
   17.33    19.99 
[1] "1.9 - 23.9 (17.3)" "0.2 - 91.7 (20.0)"
[1] "hr=" "2.4"
D1V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        2         6        1
  subtype2       1        1        4         5        1
D1V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          0        1
  STAGE IB         0        1
  STAGE II         2        4
  STAGE III        6        5
  STAGE IV         1        1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     3     6
  subtype2    10     2
D1V4, multiclass
       clus
vv      subtype1 subtype2
  T1+T2        3       10
  T3+T4        6        2
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype1  6     3
  subtype2  8     3
D1V5, multiclass
       clus
vv      subtype1 subtype2
  N0           6        8
  N1+N2        3        3
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  8  0  1
  subtype2  7  1  4
D1V6, multiclass
    clus
vv   subtype1 subtype2
  M0        8        7
  M1        0        1
  MX        1        4
[1] 3 2
[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 3 6
  subtype2 3 9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    3    9
        clus
vv       subtype1 subtype2
  FEMALE        3        3
  MALE          6        9
[1] 2 2
[1] FALSE

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2      0 1
  subtype1 3 8
  subtype2 2 8
subtype1 subtype2 
      11       10 
subtype1 subtype2 
       8        8 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       17.95         8.02        12.20        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD 
       17.33        24.89        43.27        13.61        15.09 

$subtype2
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
        1.87        31.20        80.84         5.19         3.52        10.95 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
       51.78         0.23        23.90         7.99 

subtype1 subtype2 
    8.02     0.23 
subtype1 subtype2 
   91.73    80.84 
subtype1 subtype2 
   17.95     9.47 
[1] "8.0 - 91.7 (17.9)" "0.2 - 80.8 (9.5)" 
[1] "hr=" "1.5"
D2V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       0        0        5         4        2
  subtype2       1        1        1         7        0
D2V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          0        1
  STAGE IB         0        1
  STAGE II         5        1
  STAGE III        4        7
  STAGE IV         2        0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     8     3
  subtype2     5     5
D2V4, multiclass
       clus
vv      subtype1 subtype2
  T1+T2        8        5
  T3+T4        3        5
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype1  8     3
  subtype2  6     3
D2V5, multiclass
       clus
vv      subtype1 subtype2
  N0           8        6
  N1+N2        3        3
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  7  1  3
  subtype2  8  0  2
D2V6, multiclass
    clus
vv   subtype1 subtype2
  M0        7        8
  M1        1        0
  MX        3        2
[1] 3 2
[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 3 8
  subtype2 3 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    8
  subtype2    3    7
        clus
vv       subtype1 subtype2
  FEMALE        3        3
  MALE          8        7
[1] 2 2
[1] FALSE

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 3 8
  subtype2 2 8
subtype1 subtype2 
      11       10 
subtype1 subtype2 
       8        8 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       17.95         8.02        12.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD 
       23.31        24.89        43.27        13.61        15.09 

$subtype2
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
        1.87        31.20         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
       51.78         0.23        23.90         7.99 

subtype1 subtype2 
    8.02     0.23 
subtype1 subtype2 
   91.73    51.78 
subtype1 subtype2 
   18.81     9.47 
[1] "8.0 - 91.7 (18.8)" "0.2 - 51.8 (9.5)" 
[1] "hr=" "2.3"
D3V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        5         3        2
  subtype2       0        1        1         8        0
D3V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE I          1        0
  STAGE IB         0        1
  STAGE II         5        1
  STAGE III        3        8
  STAGE IV         2        0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     9     2
  subtype2     4     6
D3V4, multiclass
       clus
vv      subtype1 subtype2
  T1+T2        9        4
  T3+T4        2        6
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype1  8     3
  subtype2  6     3
D3V5, multiclass
       clus
vv      subtype1 subtype2
  N0           8        6
  N1+N2        3        3
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  7  1  3
  subtype2  8  0  2
D3V6, multiclass
    clus
vv   subtype1 subtype2
  M0        7        8
  M1        1        0
  MX        3        2
[1] 3 2
[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 3 8
  subtype2 3 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    8
  subtype2    3    7
        clus
vv       subtype1 subtype2
  FEMALE        3        3
  MALE          8        7
[1] 2 2
[1] FALSE

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2      0 1
  subtype1 3 8
  subtype2 1 3
  subtype3 1 5
subtype1 subtype2 subtype3 
      11        4        6 
subtype1 subtype2 subtype3 
       8        3        5 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SH-A7BD 
       91.73        24.89        43.27        13.61        15.09 

$subtype2
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BR TCGA-SH-A7BC 
       18.81        23.31        51.78        23.90 

$subtype3
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-NQ-A57I TCGA-SH-A7BH 
        5.19        17.33         3.52        10.95         0.23         7.99 

subtype1 subtype2 subtype3 
    1.87    18.81     0.23 
subtype1 subtype2 subtype3 
   91.73    51.78    17.33 
subtype1 subtype2 subtype3 
  17.950   23.605    6.590 
[1] "1.9 - 91.7 (17.9)"  "18.8 - 51.8 (23.6)" "0.2 - 17.3 (6.6)"  
D4V2, continuous
          vv
clus       STAGE I STAGE IB STAGE II STAGE III STAGE IV
  subtype1       1        0        4         4        2
  subtype2       0        0        1         3        0
  subtype3       0        1        1         4        0
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          1        0        0
  STAGE IB         0        0        1
  STAGE II         4        1        1
  STAGE III        4        3        4
  STAGE IV         2        0        0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     8     3
  subtype2     3     1
  subtype3     2     4
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        8        3        2
  T3+T4        3        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"
          vv
clus       N0 N1+N2
  subtype1  8     3
  subtype2  1     3
  subtype3  5     0
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0           8        1        5
  N1+N2        3        3        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"
          vv
clus       M0 M1 MX
  subtype1  7  1  3
  subtype2  3  0  1
  subtype3  5  0  1
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        7        3        5
  M1        1        0        0
  MX        3        1        1
[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"
D4V7, binary
          cls
clus       0 1
  subtype1 3 8
  subtype2 2 2
  subtype3 1 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    8
  subtype2    2    2
  subtype3    1    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        2        1
  MALE          8        2        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2      0 1
  subtype1 2 7
  subtype2 2 5
subtype1 subtype2 
       9        7 
subtype1 subtype2 
       7        5 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL 
       17.95         1.87        31.20        18.81        23.31        10.95 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BH 
       51.78        13.61         7.99 

$subtype2
TCGA-LK-A4O5 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SH-A7BC 
       12.20         5.19        17.33         3.52         0.23        23.90 
TCGA-SH-A7BD 
       15.09 

subtype1 subtype2 
    1.87     0.23 
subtype1 subtype2 
   51.78    23.90 
subtype1 subtype2 
   17.95    12.20 
[1] "1.9 - 51.8 (17.9)" "0.2 - 23.9 (12.2)"
[1] "hr=" "1.8"
D5V2, continuous
          vv
clus       STAGE IB STAGE II STAGE III STAGE IV
  subtype1        0        3         5        1
  subtype2        1        0         5        1
D5V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE IB         0        1
  STAGE II         3        0
  STAGE III        5        5
  STAGE IV         1        1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     6     3
  subtype2     2     5
D5V4, multiclass
       clus
vv      subtype1 subtype2
  T1+T2        6        2
  T3+T4        3        5
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype1  5     4
  subtype2  5     1
D5V5, multiclass
       clus
vv      subtype1 subtype2
  N0           5        5
  N1+N2        4        1
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  7  0  2
  subtype2  5  1  1
D5V6, multiclass
    clus
vv   subtype1 subtype2
  M0        7        5
  M1        0        1
  MX        2        1
[1] 3 2
[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 4 5
  subtype2 1 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    1    6
        clus
vv       subtype1 subtype2
  FEMALE        4        1
  MALE          5        6
[1] 2 2
[1] FALSE

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2      0 1
  subtype1 1 2
  subtype2 1 2
  subtype3 1 3
subtype1 subtype2 subtype3 
       3        3        4 
subtype1 subtype2 subtype3 
       2        2        3 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A6BS 
       17.95        31.20        13.61 

$subtype2
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A6BL 
        1.87        12.20        10.95 

$subtype3
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SH-A7BC 
        5.19         3.52         0.23        23.90 

subtype1 subtype2 subtype3 
   13.61     1.87     0.23 
subtype1 subtype2 subtype3 
    31.2     12.2     23.9 
subtype1 subtype2 subtype3 
  17.950   10.950    4.355 
[1] "13.6 - 31.2 (17.9)" "1.9 - 12.2 (10.9)"  "0.2 - 23.9 (4.4)"  
D6V2, continuous
          vv
clus       STAGE IB STAGE II STAGE III STAGE IV
  subtype1        0        1         1        1
  subtype2        0        1         2        0
  subtype3        1        0         3        0
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE IB         0        0        1
  STAGE II         1        1        0
  STAGE III        1        2        3
  STAGE IV         1        0        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       T1+T2 T3+T4
  subtype1     2     1
  subtype2     1     2
  subtype3     1     3
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1+T2        2        1        1
  T3+T4        1        2        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1+N2
  subtype1  1     2
  subtype2  3     0
  subtype3  2     1
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0           1        3        2
  N1+N2        2        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 MX
  subtype1  2  1
  subtype2  3  0
  subtype3  3  1
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        2        3        3
  MX        1        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 2 1
  subtype3 0 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    2    1
  subtype3    0    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        0        2        0
  MALE          3        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"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2      0 1
  subtype1 1 7
  subtype2 3 5
subtype1 subtype2 
       8        8 
subtype1 subtype2 
       7        5 
$subtype1
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL 
       17.95         1.87        31.20        18.81        23.31        10.95 
TCGA-MQ-A6BR TCGA-SH-A7BH 
       51.78         7.99 

$subtype2
TCGA-LK-A4O5 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I 
       12.20         5.19        17.33         3.52        13.61         0.23 
TCGA-SH-A7BC TCGA-SH-A7BD 
       23.90        15.09 

subtype1 subtype2 
    1.87     0.23 
subtype1 subtype2 
   51.78    23.90 
subtype1 subtype2 
  18.380   12.905 
[1] "1.9 - 51.8 (18.4)" "0.2 - 23.9 (12.9)"
[1] "hr=" "1.5"
D7V2, continuous
          vv
clus       STAGE IB STAGE II STAGE III STAGE IV
  subtype1        0        2         5        1
  subtype2        1        1         5        1
D7V3, multiclass
           clus
vv          subtype1 subtype2
  STAGE IB         0        1
  STAGE II         2        1
  STAGE III        5        5
  STAGE IV         1        1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype1     5     3
  subtype2     3     5
D7V4, multiclass
       clus
vv      subtype1 subtype2
  T1+T2        5        3
  T3+T4        3        5
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype1  4     4
  subtype2  6     1
D7V5, multiclass
       clus
vv      subtype1 subtype2
  N0           4        6
  N1+N2        4        1
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype1  7  0  1
  subtype2  5  1  2
D7V6, multiclass
    clus
vv   subtype1 subtype2
  M0        7        5
  M1        0        1
  MX        1        2
[1] 3 2
[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 4 4
  subtype2 1 7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    4
  subtype2    1    7
        clus
vv       subtype1 subtype2
  FEMALE        4        1
  MALE          4        7
[1] 2 2
[1] FALSE

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2      0 1
  subtype2 1 2
  subtype3 1 4
subtype2 subtype3 
       3        5 
subtype2 subtype3 
       2        4 
$subtype2
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A6BL 
        1.87        12.20        10.95 

$subtype3
TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        5.19         3.52         0.23        23.90        15.09 

subtype2 subtype3 
    1.87     0.23 
subtype2 subtype3 
    12.2     23.9 
subtype2 subtype3 
   10.95     5.19 
[1] "1.9 - 12.2 (10.9)" "0.2 - 23.9 (5.2)" 
[1] "hr=" "1.4"
D8V2, continuous
          vv
clus       STAGE IB STAGE II STAGE III STAGE IV
  subtype2        0        1         2        0
  subtype3        1        0         3        1
D8V3, multiclass
           clus
vv          subtype2 subtype3
  STAGE IB         0        1
  STAGE II         1        0
  STAGE III        2        3
  STAGE IV         0        1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1+T2 T3+T4
  subtype2     1     2
  subtype3     2     3
D8V4, multiclass
       clus
vv      subtype2 subtype3
  T1+T2        1        2
  T3+T4        2        3
[1] 2 2
[1] FALSE
          vv
clus       N0 N1+N2
  subtype2  3     0
  subtype3  3     1
D8V5, multiclass
       clus
vv      subtype2 subtype3
  N0           3        3
  N1+N2        0        1
[1] 2 2
[1] FALSE
          vv
clus       M0 M1 MX
  subtype2  3  0  0
  subtype3  3  1  1
D8V6, multiclass
    clus
vv   subtype2 subtype3
  M0        3        3
  M1        0        1
  MX        0        1
[1] 3 2
[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
  subtype2 2 1
  subtype3 0 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    2    1
  subtype3    0    5
        clus
vv       subtype2 subtype3
  FEMALE        2        0
  MALE          1        5
[1] 2 2
[1] FALSE
