
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.32.3479/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.32.3479/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP/1552814/1.GDAC_mergedClustering.Finished/KIRP.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1445475/1.GDAC_clinicalDataPicker.Finished/KIRP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=1", "-MF=ALL", "-oT=", "-nV=Nozzle.R1", "-OP=AGGREGRATED_CLUSTER", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"                     "-OP=AGGREGRATED_CLUSTER"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  

nPatients in clinical file=95, in cluster file=97, common to both=95
[1]  7 95
[1] "MRNA_CNMF"
[1] 3
1 2 
7 9 
1 2 
7 9 
[1] "MRNA_CHIERARCHICAL"
[1] 3
1 2 3 
4 7 5 
1 2 3 
4 7 5 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
36 19 24 
 1  2  3 
36 19 24 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
22 18 12 11 
 1  2  3  4 
22 18 12 11 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
16 25 22 
 1  2  3 
16 25 22 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
14 15 14 
 1  2  3 
14 15 14 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
13 15 15 
 1  2  3 
13 15 15 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NEOADJUVANTTHERAPY"                    
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 95 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7734 TCGA-A4-7828 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
          27           NA          293         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
         922          763         1357          336          109          125 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         179          135         1536           21          329           92 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
          14           33           19          196           36         2638 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         585          269         1938          697         1313         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
         658         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403          329          232           29          364          240 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3759           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1532         1516          799          612           NA 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          213          217          115          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          418          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
         445           92         2428         2459         1556         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
        1669          471          178          160          208          977 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
        1257           NA          928         1059          387         5558 
TCGA-GL-7773 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-J7-6720 
          NA           NA           NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=79,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 95 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=37, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
54 10 30  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   54    10    31 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
54 10 30  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   54    10    31 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
19 10  4 
[1] "table(vv)"
vv
N0 N1 N2 
19 10  4 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 
19 10  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
19 10  4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
 [1] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[13] "subtype2" "subtype2" "subtype1" "subtype2"
[1] "hr=" "1.8"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    6    3
        clus
vv       subtype1 subtype2
  FEMALE        1        3
  MALE          6        6
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       1 
character(0)
D1V5, multiclass
D1V6, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 
       2 
character(0)
D1V7, multiclass
    clus
vv   subtype1 subtype2
  M0        4        5
  M1        1        0

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
 [1] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype1" "subtype3"
[13] "subtype1" "subtype2" "subtype2" "subtype3"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    1
  subtype2    5    2
  subtype3    4    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        1        2        1
  MALE          3        5        4
D2V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)
D2V5, multiclass
D2V6, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       2 
character(0)
D2V7, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        5        3 
[1] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[8] "subtype2"
    clus
vv   subtype2 subtype3
  M0        4        3
  M1        1        0

Clustering(3) Variable = METHLYATION_CNMF
D3V1, survival
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[19] "subtype3" "subtype2" "subtype2" "subtype1" "subtype3" "subtype3"
[25] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[61] "subtype1" "subtype1" "subtype1" "subtype2" "subtype3" "subtype1"
[67] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
D3V2, continuous
D3V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    8
  subtype2   12    7
  subtype3   15    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8        7        9
  MALE         28       12       15
D3V4, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
      14        4        1 
 [1] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass

Clustering(4) Variable = MRNASEQ_CNMF
D4V1, survival
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[37] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype4" "subtype3" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype1" "subtype4" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype1"
[61] "subtype3" "subtype1" "subtype2"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   11
  subtype2   12    6
  subtype3   11    1
  subtype4    9    2
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       11        6        1        2
  MALE         11       12       11        9
D4V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        3        1        2 
[1] "subtype2" "subtype2" "subtype2"
D4V5, multiclass
D4V6, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      15        3        7        1 
 [1] "subtype1" "subtype3" "subtype1" "subtype2" "subtype1" "subtype3"
 [7] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype3"
[13] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[19] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[25] "subtype2"
D4V7, multiclass

Clustering(5) Variable = MRNASEQ_CHIERARCHICAL
D5V1, survival
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
 [1] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
 [7] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[19] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[25] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[31] "subtype1" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[43] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
[55] "subtype3" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype2" "subtype1" "subtype2"
D5V2, continuous
D5V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2   19    6
  subtype3   17    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        6        5
  MALE          7       19       17
D5V4, continuous
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass

Clustering(6) Variable = MIRSEQ_CNMF
D6V1, survival
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype3"
 [1] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [7] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[13] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype3"
[25] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[31] "subtype1" "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[43] "subtype3"
D6V2, continuous
D6V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10    4
  subtype2   11    4
  subtype3    9    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        4        5
  MALE         10       11        9
D6V4, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       1        5 
[1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
D6V5, multiclass
D6V6, multiclass
    clus
vv   subtype1 subtype3
  N0        6        1
  N1        3        6
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       13        8        9
  M1        0        0        5

Clustering(7) Variable = MIRSEQ_CHIERARCHICAL
D7V1, survival
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1"
 [1] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[43] "subtype1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    5
  subtype2   12    3
  subtype3   10    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        3        5
  MALE          8       12       10
D7V4, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       4        1        1 
[1] "subtype1" "subtype1" "subtype1" "subtype1"
D7V5, multiclass
D7V6, multiclass
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       6        9        1 
 [1] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[13] "subtype2" "subtype1" "subtype1"
    clus
vv   subtype1 subtype2
  N0        1        6
  N1        5        3
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        9       13        8
  M1        4        1        0
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
                "PATHOLOGY.T"                 "PATHOLOGY.N" 
                           V7 
        "PATHOLOGICSPREAD(M)" 
> q(save="no")
