
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/8282693/ESCA-TP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/8142806/ESCA-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=.05", "-cQ=0.25", "-MF=ALL", "-oT=ESCA-TP", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=ESCA-TP"
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/8142806/ESCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/8282693/ESCA-TP.mergedcluster.txt"

nPatients in clinical file=57, in cluster file=126, common to both=57
[1]  8 57
[1] "CN_CNMF"
[1] 3
 1  2  3 
15 26 15 
 1  2  3 
15 26 15 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
17 27 13 
 1  2  3 
17 27 13 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
 9 21  5 16 
 1  2  3  4 
 9 21  5 16 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
17  3 31 
 1  2  3 
17  3 31 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
24 11 17 
 1  2  3 
24 11 17 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
 1 17 34 
 2  3 
17 34 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
10  5 21 16 
 1  2  3  4 
10  5 21 16 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
 1 17 34 
 2  3 
17 34 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NUMBERPACKYEARSSMOKED"                 
[13] "GLEASON_SCORE"                         
[14] "PSA_VALUE"                             
[15] "DAYS_TO_PSA"                           
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 57 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
         611           NA          632           80          612            1 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
           8           30           16           NA           NA           11 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
           4           34           NA          107          112          102 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
         124           NA          101          218           NA           NA 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A891 
         935           NA          882           NA           NA          120 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
         266            5            2           10           NA            3 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
           4            2            3            2            3            2 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
          NA            4            2            3            3            3 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-Q9-A6FW 
           2            2            3            2           NA          115 
TCGA-R6-A6DQ TCGA-S8-A6BV TCGA-S8-A6BW 
          NA          267          426 
Variable 1:'AGE':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	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=5,	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:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'NUMBERPACKYEARSSMOKED':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=8,	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"               
[7] "NUMBERPACKYEARSSMOKED"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 57 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=33, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 15 32  3 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    6    15    35 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 6 15 32  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    6    15    35 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
27 20  6  2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   27    20     8 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
27 20  6  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   27    20     8 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=17, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 11  3
  subtype2 22  2
  subtype3  7  8
subtype1 subtype2 subtype3 
      14       24       15 
subtype1 subtype2 subtype3 
       3        2        8 
$subtype1
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-L5-A4OF 
        0.85        20.12         0.99         0.79         1.12         3.68 
TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-LN-A49X TCGA-LN-A4A5 
        3.35         3.32         7.17        30.74         0.10         0.10 
TCGA-Q9-A6FW TCGA-S8-A6BV 
        3.78         8.78 

$subtype2
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         0.03         0.53         0.36         0.13 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
        4.31         4.08        29.00         0.16         0.07         0.10 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.13         0.07         0.07         0.13         0.07         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.10         0.07         0.07         0.07         5.16        14.01 

$subtype3
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
       20.09         0.26         3.52        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49U 
        4.90         7.13         7.43         8.75         0.33         0.07 
TCGA-LN-A49V TCGA-LN-A4MQ TCGA-R6-A6DQ 
        0.10         0.10         7.59 

subtype1 subtype2 subtype3 
    0.10     0.03     0.07 
subtype1 subtype2 subtype3 
   30.74    29.00    20.09 
subtype1 subtype2 subtype3 
   3.335    0.130    3.520 
[1] "0.1 - 30.7 (3.3)" "0.0 - 29.0 (0.1)" "0.1 - 20.1 (3.5)"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
 [1] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype1" "subtype2" "subtype3" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[31] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[37] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[43] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[49] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        1        1        0         4         2         0
  subtype2       0        1        1        1         9         5         4
  subtype3       0        1        0        0         3         4         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          4          1          1        0
  subtype2          3          2          0        0
  subtype3          1          2          1        1
D1V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  3  2    10
  subtype2  1 10    15
  subtype3  2  3     9
D1V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  8  4     2
  subtype2 14 10     2
  subtype3  5  5     4
D1V5, multiclass
          vv
clus       M0 M1A MX
  subtype1 11   0  3
  subtype2 23   0  2
  subtype3  8   1  3
D1V6, multiclass
D1V7, binary
          cls
clus        0  1
  subtype1  4 11
  subtype2  2 24
  subtype3  2 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   11
  subtype2    2   24
  subtype3    2   13
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        2        2
  MALE         11       24       13
D1V8, continuous

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 10  7
  subtype2 22  3
  subtype3  9  3
subtype1 subtype2 subtype3 
      17       25       12 
subtype1 subtype2 subtype3 
       7        3        3 
$subtype1
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         3.16         4.90        29.00         7.13         7.43 
TCGA-L5-A891 TCGA-L7-A6VZ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        3.95         8.75         3.78         7.59         8.78 

$subtype2
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
       20.09         0.85         2.63         0.53         0.36         0.13 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        4.31         4.08         0.16         0.07         0.33         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.13         0.07         0.10         0.07         0.13         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU 
        0.10         0.07         0.07         0.10         0.07         5.16 
TCGA-S8-A6BW 
       14.01 

$subtype3
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP 
       20.78        20.12         0.03         0.99         0.79         1.12 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 
        1.38        30.74         0.07         0.10         0.07         0.10 

subtype1 subtype2 subtype3 
    0.26     0.07     0.03 
subtype1 subtype2 subtype3 
   29.00    20.09    30.74 
subtype1 subtype2 subtype3 
    4.90     0.13     0.89 
[1] "0.3 - 29.0 (4.9)" "0.1 - 20.1 (0.1)" "0.0 - 30.7 (0.9)"
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype2" "subtype3" "subtype2" "subtype2"
[13] "subtype3" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[49] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        2        0        0         1         4         0
  subtype2       0        1        1        1        11         5         3
  subtype3       0        0        1        0         4         2         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          1          3          2        1
  subtype2          3          2          0        0
  subtype3          4          0          0        0
D2V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  5  2     9
  subtype2  1  9    17
  subtype3  0  4     9
D2V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  4  7     5
  subtype2 17  8     2
  subtype3  6  5     1
D2V5, multiclass
          vv
clus       M0 M1A MX
  subtype1  8   1  4
  subtype2 24   0  2
  subtype3 11   0  2
D2V6, multiclass
D2V7, binary
          cls
clus        0  1
  subtype1  4 13
  subtype2  2 25
  subtype3  2 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   13
  subtype2    2   25
  subtype3    2   11
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        2        2
  MALE         13       25       11
D2V8, continuous

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1  7  1
  subtype2 16  4
  subtype3  5  0
  subtype4  8  8
subtype1 subtype2 subtype3 subtype4 
       8       20        5       16 
subtype1 subtype2 subtype3 subtype4 
       1        4        0        8 
$subtype1
TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A625 TCGA-L5-A4OM TCGA-LN-A49V TCGA-LN-A49Y 
       20.78         0.99         0.36         4.08         0.10         0.07 
TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.07 

$subtype2
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A43J TCGA-LN-A49M 
       20.09         0.85         0.53         0.79         4.31         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.07         0.33         0.10         0.07         0.07         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR 
        0.13         0.07         0.10         0.10         0.07         0.07 
TCGA-Q9-A6FU TCGA-S8-A6BW 
        5.16        14.01 

$subtype3
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-LN-A49S TCGA-LN-A4MQ TCGA-Q9-A6FW 
       20.12         0.03         0.13         0.10         3.78 

$subtype4
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.13         7.43         7.59         8.78 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 
   20.78    20.09    20.12    30.74 
subtype1 subtype2 subtype3 subtype4 
   0.230    0.115    0.130    6.015 
[1] "0.1 - 20.8 (0.2)" "0.1 - 20.1 (0.1)" "0.0 - 20.1 (0.1)" "0.3 - 30.7 (6.0)"
 [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[43] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
[49] "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[43] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
[49] "subtype2"
 [1] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype4"
 [7] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype4"
[13] "subtype4" "subtype4" "subtype1" "subtype4" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[31] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[43] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
[49] "subtype2"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        0        0         6         0         0
  subtype2       0        0        2        1         8         3         4
  subtype3       0        0        0        0         1         1         1
  subtype4       1        2        0        0         1         5         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          1          1          0        0
  subtype2          2          1          0        0
  subtype3          1          1          0        0
  subtype4          2          2          1        1
D3V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  2     6
  subtype2  0  6    15
  subtype3  0  1     4
  subtype4  5  4     6
D3V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  8  0     1
  subtype2 14  6     1
  subtype3  1  3     1
  subtype4  4  7     4
D3V5, multiclass
          vv
clus       M0 M1A MX
  subtype1  8   0  0
  subtype2 19   0  2
  subtype3  5   0  0
  subtype4  7   1  4
D3V6, multiclass
D3V7, binary
          cls
clus        0  1
  subtype1  1  8
  subtype2  1 20
  subtype3  0  5
  subtype4  5 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    8
  subtype2    1   20
  subtype3    0    5
  subtype4    5   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        1        1        0        5
  MALE          8       20        5       11
D3V8, continuous

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  9  8
  subtype2  2  1
  subtype3 25  4
subtype1 subtype2 subtype3 
      17        3       29 
subtype1 subtype2 subtype3 
       8        1        4 
$subtype1
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.13         7.43         3.78         7.59         8.78 

$subtype2
TCGA-IG-A4QT TCGA-LN-A49V TCGA-LN-A4A8 
        0.99         0.10         0.07 

$subtype3
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       20.09         0.85        20.78        20.12         0.03         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A43J TCGA-L5-A4OM TCGA-LN-A49M TCGA-LN-A49N 
        0.79         0.36         4.31         4.08         0.16         0.07 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
        0.33         0.10         0.13         0.07         0.07         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
        0.07         0.13         0.07         0.10         0.10         0.10 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.07         0.10         0.07         5.16        14.01 

subtype1 subtype2 subtype3 
    0.26     0.07     0.03 
subtype1 subtype2 subtype3 
   30.74     0.99    20.78 
subtype1 subtype2 subtype3 
    4.90     0.10     0.13 
[1] "0.3 - 30.7 (4.9)" "0.1 - 1.0 (0.1)"  "0.0 - 20.8 (0.1)"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[43] "subtype3" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        2        0        0         1         5         0
  subtype2       0        0        0        0         3         0         0
  subtype3       0        1        2        1        12         4         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          2          3          1        1
  subtype2          0          0          0        0
  subtype3          4          2          0        0
D4V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  5  4     7
  subtype2  0  1     2
  subtype3  1  8    22
D4V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  4  7     5
  subtype2  3  0     0
  subtype3 20  9     2
D4V5, multiclass
          vv
clus       M0 M1A MX
  subtype1  8   1  4
  subtype2  3   0  0
  subtype3 28   0  2
D4V6, multiclass
D4V7, binary
          cls
clus        0  1
  subtype1  5 12
  subtype2  0  3
  subtype3  2 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   12
  subtype2    0    3
  subtype3    2   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        0        2
  MALE         12        3       29
D4V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
      11        2       19 
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 19  3
  subtype2  8  2
  subtype3  9  8
subtype1 subtype2 subtype3 
      22       10       17 
subtype1 subtype2 subtype3 
       3        2        8 
$subtype1
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-L5-A43J 
       20.09        20.12         0.03         0.53         0.79         4.31 
TCGA-L5-A4OM TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        4.08         0.16         0.33         0.10         0.13         0.07 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.07         0.13         0.07         0.10         0.10         0.07 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-Q9-A6FU TCGA-S8-A6BW 
        0.07         0.07         5.16        14.01 

$subtype2
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A625 TCGA-LN-A49N 
        0.85        20.78         2.63         0.99         0.36         0.07 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4MQ 
        0.07         0.10         0.10         0.10 

$subtype3
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.13         7.43         3.78         7.59         8.78 

subtype1 subtype2 subtype3 
    0.03     0.07     0.26 
subtype1 subtype2 subtype3 
   20.12    20.78    30.74 
subtype1 subtype2 subtype3 
    0.13     0.23     4.90 
[1] "0.0 - 20.1 (0.1)" "0.1 - 20.8 (0.2)" "0.3 - 30.7 (4.9)"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[49] "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[49] "subtype1"
 [1] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [7] "subtype3" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[13] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype1" "subtype3" "subtype3" "subtype3"
[49] "subtype1"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        2        1        10         4         3
  subtype2       0        0        0        0         4         1         2
  subtype3       1        2        0        0         1         5         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          2          1          0        0
  subtype2          3          1          0        0
  subtype3          2          3          1        1
D5V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  1  8    15
  subtype2  0  2     9
  subtype3  5  4     7
D5V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1 16  7     1
  subtype2  6  4     1
  subtype3  4  7     5
D5V5, multiclass
          vv
clus       M0 M1A MX
  subtype1 21   0  2
  subtype2 11   0  0
  subtype3  8   1  4
D5V6, multiclass
D5V7, binary
          cls
clus        0  1
  subtype1  2 22
  subtype2  0 11
  subtype3  5 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   22
  subtype2    0   11
  subtype3    5   12
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        2        0        5
  MALE         22       11       12
D5V8, continuous

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype2  9  8
  subtype3 27  4
subtype2 subtype3 
      17       31 
subtype2 subtype3 
       8        4 
$subtype2
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.13         7.43         3.78         7.59         8.78 

$subtype3
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A43J TCGA-L5-A4OM TCGA-LN-A49M 
        0.53         0.79         0.36         4.31         4.08         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.07         0.33         0.10         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU 
        0.10         0.07         0.07         0.10         0.07         5.16 
TCGA-S8-A6BW 
       14.01 

subtype2 subtype3 
    0.26     0.03 
subtype2 subtype3 
   30.74    20.78 
subtype2 subtype3 
    4.90     0.13 
[1] "0.3 - 30.7 (4.9)" "0.0 - 20.8 (0.1)"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[1] "hr=" "1.3"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype2       1        2        0        0         1         5         0
  subtype3       0        1        2        1        13         5         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype2          2          3          1        1
  subtype3          5          2          0        0
D6V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype2  5  4     7
  subtype3  1 10    23
D6V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype2  4  7     5
  subtype3 21 11     2
D6V5, multiclass
          vv
clus       M0 M1A MX
  subtype2  8   1  4
  subtype3 31   0  2
D6V6, multiclass
D6V7, binary
          cls
clus        0  1
  subtype2  5 12
  subtype3  2 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    5   12
  subtype3    2   32
        clus
vv       subtype2 subtype3
  FEMALE        5        2
  MALE         12       32
D6V8, continuous

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1  8  1
  subtype2  4  1
  subtype3 16  3
  subtype4  8  8
subtype1 subtype2 subtype3 subtype4 
       9        5       19       16 
subtype1 subtype2 subtype3 subtype4 
       1        1        3        8 
$subtype1
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A50L TCGA-LN-A49N TCGA-LN-A49W 
        0.85        20.78         2.63         0.53         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A4A5 TCGA-LN-A4MQ 
        0.10         0.10         0.10 

$subtype2
TCGA-IG-A3QL TCGA-IG-A4QT TCGA-L5-A4OF TCGA-L5-A4OM TCGA-LN-A4A8 
       20.09         0.99         3.68         4.08         0.07 

$subtype3
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A43J TCGA-LN-A49M 
       20.12         0.03         0.79         0.36         4.31         0.16 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A2 
        0.33         0.10         0.13         0.07         0.07         0.13 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-Q9-A6FU 
        0.07         0.10         0.10         0.07         0.07         5.16 
TCGA-S8-A6BW 
       14.01 

$subtype4
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        0.26         3.52         3.35        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        30.74         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.43         3.78         7.59         8.78 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 
   20.78    20.09    20.12    30.74 
subtype1 subtype2 subtype3 subtype4 
   0.100    3.680    0.130    6.015 
[1] "0.1 - 20.8 (0.1)" "0.1 - 20.1 (3.7)" "0.0 - 20.1 (0.1)" "0.3 - 30.7 (6.0)"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype1" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
[49] "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype1" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
[49] "subtype3"
 [1] "subtype2" "subtype1" "subtype1" "subtype1" "subtype3" "subtype3"
 [7] "subtype4" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[13] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype4" "subtype3" "subtype1" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[43] "subtype1" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
[49] "subtype3"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        0        0         3         1         2
  subtype2       0        1        0        0         2         2         0
  subtype3       0        0        2        1         9         3         3
  subtype4       1        2        0        0         1         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          4          0          0        0
  subtype2          0          0          0        0
  subtype3          1          2          0        0
  subtype4          2          3          1        1
D7V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype1  0  2     8
  subtype2  2  1     2
  subtype3  0  7    14
  subtype4  4  4     7
D7V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype1  5  5     0
  subtype2  4  1     0
  subtype3 13  6     2
  subtype4  4  6     5
D7V5, multiclass
          vv
clus       M0 M1A MX
  subtype1 10   0  0
  subtype2  3   0  0
  subtype3 19   0  2
  subtype4  8   1  4
D7V6, multiclass
D7V7, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2  1  4
  subtype3  1 20
  subtype4  5 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2    1    4
  subtype3    1   20
  subtype4    5   11
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        0        1        1        5
  MALE         10        4       20       11
D7V8, continuous

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype2  9  8
  subtype3 27  4
subtype2 subtype3 
      17       31 
subtype2 subtype3 
       8        4 
$subtype2
TCGA-IG-A4QS TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO 
        0.26         3.52         3.68         3.35        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        30.74         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-S8-A6BV 
        7.13         7.43         3.78         7.59         8.78 

$subtype3
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12         0.03 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A43J TCGA-L5-A4OM TCGA-LN-A49M 
        0.53         0.79         0.36         4.31         4.08         0.16 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        0.07         0.33         0.10         0.13         0.07         0.07 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10         0.07         0.13         0.07         0.10         0.10 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-Q9-A6FU 
        0.10         0.07         0.07         0.10         0.07         5.16 
TCGA-S8-A6BW 
       14.01 

subtype2 subtype3 
    0.26     0.03 
subtype2 subtype3 
   30.74    20.78 
subtype2 subtype3 
    4.90     0.13 
[1] "0.3 - 30.7 (4.9)" "0.0 - 20.8 (0.1)"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
 [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[19] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[43] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[1] "hr=" "1.3"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype2       1        2        0        0         1         5         0
  subtype3       0        1        2        1        13         5         5
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype2          2          3          1        1
  subtype3          5          2          0        0
D8V3, multiclass
          vv
clus       T1 T2 T3+T4
  subtype2  5  4     7
  subtype3  1 10    23
D8V4, multiclass
          vv
clus       N0 N1 N2+N3
  subtype2  4  7     5
  subtype3 21 11     2
D8V5, multiclass
          vv
clus       M0 M1A MX
  subtype2  8   1  4
  subtype3 31   0  2
D8V6, multiclass
D8V7, binary
          cls
clus        0  1
  subtype2  5 12
  subtype3  2 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype2    5   12
  subtype3    2   32
        clus
vv       subtype2 subtype3
  FEMALE        5        2
  MALE         12       32
D8V8, continuous
> q(save="no")
