
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/LUAD/1591469/1.GDAC_mergedClustering.Finished/LUAD.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1552288/1.GDAC_clinicalDataPicker.Finished/LUAD.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=292, in cluster file=287, common to both=283
[1]   7 283
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
 5  9 12  6 
 1  2  3  4 
 5  9 12  6 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
 7 13 12 
 1  2  3 
 7 13 12 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
52 60 52 52 
 1  2  3  4 
52 60 52 52 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
88 68 84 
 1  2  3 
88 68 84 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
25 12 49 23 56 75 
 1  2  3  4  5  6 
25 12 49 23 56 75 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
39 29 32 
 1  2  3 
39 29 32 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
40 31 29 
 1  2  3 
40 31 29 
[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 283 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1158          121          606          426           NA 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA          303           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
          NA          610           NA           90          454           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         911           NA          913           NA          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730          457           31          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
          90           NA           30           62           14          224 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         181          264         1448         2595         1147         1491 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         863         1073          354         1357          158           NA 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
         574          581          400          529          103          480 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
         400           97          246          311          253          196 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         189          140          106          498          208            9 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         102          302          236           95          165           82 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938           NA         1110           NA          298          162 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         153           50          557           NA          531          535 
TCGA-44-7672 TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
         418         2318           NA           NA           NA         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896           NA 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1314          457          369          395          150            1 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
          NA           NA         2174         1485          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         297         1499          245          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        2369          653          257          460          285          135 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
         373          349           NA           NA           NA           NA 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 
          NA           NA         1015           NA          255         1068 
TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         970          701         1178         1479         1374           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
           2          992           24           NA         1238           NA 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
          28         1475           NA           NA           NA           67 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
          NA           NA         1826           NA         1233         2161 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
        1170           61           18           34           NA            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 
          95           40           39           31           31           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-64-1676 TCGA-64-1677 
          16          197           21            3         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1685         1126           NA         2550            3 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
         926          507         1145          223           30           60 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
          18           62           18           NA           27           21 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          154          186          690          414          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
          61         1599          711          911          467           14 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 
          40          122           38           NA           NA           NA 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093           NA         1201          760           NA           NA 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
          NA           NA         1220          678          214           NA 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        6812           NA           NA           NA           NA           NA 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 
          NA          327          881           NA          994           NA 
TCGA-80-5608 TCGA-80-5611 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
          NA           NA           NA           NA           11           27 
TCGA-86-7713 TCGA-86-7714 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
           7           NA           37           NA            1           39 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          35           11           NA          819          127           28 
TCGA-91-7771 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-97-7546 
          31          127           34            2          163          963 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        1435         1476         1331          263          181           NA 
TCGA-99-7458 
         250 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=80,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=173,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=6,	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=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=70,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "HISTOLOGICAL.TYPE"                     
[5] "PATHOLOGY.T"                           
[6] "PATHOLOGY.N"                           
[7] "PATHOLOGICSPREAD(M)"                   
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "5"          
[1] "PATHOLOGY.N" "6"          
Output Data has 283 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 76 167  23  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 76 167  23  15 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
 T1  T2  T3  T4 
 76 167  23  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 76 167  23  15 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
165  59  51   1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  165    59    52 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
 N0  N1  N2  N3 
165  59  51   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  165    59    52 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
[25] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype3"
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
[25] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype3"
 [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [7] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype3"
[19] "subtype4" "subtype4" "subtype1" "subtype4" "subtype2" "subtype4"
[25] "subtype4" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
[31] "subtype3"
D1V2, continuous
D1V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    3
  subtype2    6    3
  subtype3    3    9
  subtype4    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        3        9        3
  MALE          2        6        3        3
D1V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype4 
       1        1        1 
character(0)
D1V5, multiclass
D1V6, multiclass
D1V7, multiclass
D1V8, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        4        9       11        6
  M1        1        0        1        0
D1V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    9    0
  subtype3   11    1
  subtype4    6    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        0        1        0
  YES        5        9       11        6
D1V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    1
  subtype2    8    1
  subtype3    9    3
  subtype4    5    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        3        1
  YES        4        8        9        5

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2"
 [1] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
 [7] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[25] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[31] "subtype2"
D2V2, continuous
D2V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    4
  subtype2    4    9
  subtype3    7    5
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        4        9        5
  MALE          3        4        7
D2V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        2 
character(0)
D2V5, multiclass
D2V6, multiclass
D2V7, multiclass
D2V8, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0        7       12       11
  M1        0        1        1
D2V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    0
  subtype2   12    1
  subtype3   12    0
     clus
vv    subtype1 subtype2 subtype3
  NO         0        1        0
  YES        7       12       12
D2V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2   10    3
  subtype3   10    2
     clus
vv    subtype1 subtype2 subtype3
  NO         1        3        2
  YES        6       10       10

Clustering(3) Variable = METHLYATION_CNMF
D3V1, survival
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype4"
 [13] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [19] "subtype4" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [25] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype1"
 [31] "subtype4" "subtype4" "subtype4" "subtype1" "subtype2" "subtype4"
 [37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [49] "subtype4" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype4" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype4" "subtype1" "subtype1" "subtype1" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
 [79] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [91] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[109] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype2" "subtype4" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype4" "subtype1" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[139] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[151] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[157] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[163] "subtype2" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[169] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype4"
[175] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[181] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype3"
[187] "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype4"
 [13] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [19] "subtype4" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [25] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype1"
 [31] "subtype4" "subtype4" "subtype4" "subtype1" "subtype2" "subtype4"
 [37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [49] "subtype4" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype4" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype4" "subtype1" "subtype1" "subtype1" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
 [79] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [91] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[109] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype2" "subtype4" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype4" "subtype1" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[139] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[151] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[157] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[163] "subtype2" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[169] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype4"
[175] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[181] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype3"
[187] "subtype1" "subtype1"
  [1] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
  [7] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype4"
 [13] "subtype3" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
 [19] "subtype4" "subtype4" "subtype2" "subtype1" "subtype2" "subtype4"
 [25] "subtype1" "subtype3" "subtype1" "subtype4" "subtype1" "subtype1"
 [31] "subtype4" "subtype4" "subtype4" "subtype1" "subtype2" "subtype4"
 [37] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
 [43] "subtype4" "subtype3" "subtype4" "subtype1" "subtype4" "subtype2"
 [49] "subtype4" "subtype4" "subtype3" "subtype3" "subtype1" "subtype4"
 [55] "subtype4" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
 [61] "subtype4" "subtype2" "subtype2" "subtype3" "subtype1" "subtype2"
 [67] "subtype4" "subtype1" "subtype1" "subtype1" "subtype2" "subtype4"
 [73] "subtype2" "subtype4" "subtype1" "subtype1" "subtype4" "subtype3"
 [79] "subtype2" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
 [85] "subtype2" "subtype3" "subtype2" "subtype4" "subtype2" "subtype4"
 [91] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype4"
[103] "subtype3" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[109] "subtype1" "subtype3" "subtype4" "subtype3" "subtype3" "subtype2"
[115] "subtype3" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
[121] "subtype1" "subtype2" "subtype4" "subtype1" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype4" "subtype1" "subtype2" "subtype3"
[133] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[139] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[151] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[157] "subtype3" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[163] "subtype2" "subtype3" "subtype4" "subtype2" "subtype3" "subtype2"
[169] "subtype4" "subtype2" "subtype4" "subtype3" "subtype2" "subtype4"
[175] "subtype1" "subtype2" "subtype1" "subtype3" "subtype2" "subtype3"
[181] "subtype1" "subtype1" "subtype4" "subtype1" "subtype3" "subtype3"
[187] "subtype1" "subtype1"
D3V2, continuous
D3V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   35
  subtype2   37   23
  subtype3   26   26
  subtype4   21   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       23       26       31
  MALE         17       37       26       21
D3V4, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
       7        4        5        2 
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
 [7] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype1"
D3V5, multiclass
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass
D3V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    0
  subtype2   58    2
  subtype3   51    1
  subtype4   46    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        2        1        6
  YES       52       58       51       46
D3V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   11
  subtype2   55    5
  subtype3   45    7
  subtype4   44    8
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11        5        7        8
  YES       41       55       45       44

Clustering(4) Variable = MRNASEQ_CNMF
D4V1, survival
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[145] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[151] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[163] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[169] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[175] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[181] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[187] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[193] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[199] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[205] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[211] "subtype1" "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[145] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[151] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[163] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[169] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[175] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[181] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[187] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[193] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[199] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[205] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[211] "subtype1" "subtype1" "subtype2" "subtype1"
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype1"
  [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [13] "subtype2" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
 [19] "subtype3" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [25] "subtype2" "subtype2" "subtype3" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [37] "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
 [49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype3"
 [61] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [67] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype2"
 [73] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
 [79] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [85] "subtype2" "subtype1" "subtype3" "subtype1" "subtype2" "subtype1"
 [91] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [97] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[103] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[109] "subtype1" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[115] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[133] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[139] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
[145] "subtype1" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[151] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[157] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[163] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[169] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[175] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[181] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[187] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype1"
[193] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[199] "subtype3" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[205] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype1"
[211] "subtype1" "subtype1" "subtype2" "subtype1"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   62
  subtype2   30   38
  subtype3   54   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       62       38       30
  MALE         26       30       54
D4V4, continuous
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
D4V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84    4
  subtype2   65    3
  subtype3   80    4
     clus
vv    subtype1 subtype2 subtype3
  NO         4        3        4
  YES       84       65       80
D4V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75   13
  subtype2   55   13
  subtype3   73   11
     clus
vv    subtype1 subtype2 subtype3
  NO        13       13       11
  YES       75       55       73

Clustering(5) Variable = MRNASEQ_CHIERARCHICAL
D5V1, survival
  [1] "subtype6" "subtype5" "subtype4" "subtype3" "subtype5" "subtype6"
  [7] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [13] "subtype6" "subtype5" "subtype6" "subtype3" "subtype2" "subtype2"
 [19] "subtype1" "subtype6" "subtype1" "subtype2" "subtype6" "subtype4"
 [25] "subtype5" "subtype5" "subtype3" "subtype6" "subtype6" "subtype5"
 [31] "subtype5" "subtype3" "subtype6" "subtype4" "subtype6" "subtype6"
 [37] "subtype6" "subtype5" "subtype5" "subtype6" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype6" "subtype5" "subtype3" "subtype3"
 [49] "subtype6" "subtype2" "subtype6" "subtype6" "subtype3" "subtype6"
 [55] "subtype4" "subtype5" "subtype3" "subtype1" "subtype6" "subtype3"
 [61] "subtype5" "subtype5" "subtype3" "subtype3" "subtype2" "subtype4"
 [67] "subtype6" "subtype4" "subtype6" "subtype6" "subtype6" "subtype5"
 [73] "subtype6" "subtype6" "subtype1" "subtype1" "subtype4" "subtype6"
 [79] "subtype1" "subtype1" "subtype3" "subtype6" "subtype5" "subtype5"
 [85] "subtype5" "subtype6" "subtype3" "subtype6" "subtype5" "subtype6"
 [91] "subtype1" "subtype3" "subtype4" "subtype5" "subtype6" "subtype1"
 [97] "subtype1" "subtype6" "subtype6" "subtype6" "subtype3" "subtype5"
[103] "subtype3" "subtype1" "subtype6" "subtype5" "subtype5" "subtype6"
[109] "subtype2" "subtype3" "subtype3" "subtype6" "subtype3" "subtype3"
[115] "subtype5" "subtype1" "subtype3" "subtype6" "subtype3" "subtype5"
[121] "subtype3" "subtype3" "subtype1" "subtype6" "subtype4" "subtype1"
[127] "subtype5" "subtype5" "subtype5" "subtype6" "subtype2" "subtype6"
[133] "subtype6" "subtype6" "subtype6" "subtype6" "subtype6" "subtype6"
[139] "subtype5" "subtype5" "subtype5" "subtype3" "subtype5" "subtype6"
[145] "subtype6" "subtype3" "subtype3" "subtype6" "subtype3" "subtype1"
[151] "subtype5" "subtype6" "subtype3" "subtype6" "subtype6" "subtype4"
[157] "subtype6" "subtype6" "subtype5" "subtype3" "subtype6" "subtype5"
[163] "subtype1" "subtype4" "subtype5" "subtype4" "subtype6" "subtype5"
[169] "subtype5" "subtype6" "subtype1" "subtype4" "subtype1" "subtype4"
[175] "subtype4" "subtype1" "subtype3" "subtype4" "subtype6" "subtype3"
[181] "subtype1" "subtype3" "subtype4" "subtype6" "subtype1" "subtype4"
[187] "subtype1" "subtype5" "subtype3" "subtype4" "subtype6" "subtype2"
[193] "subtype5" "subtype4" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype2" "subtype3" "subtype6" "subtype5" "subtype3" "subtype4"
[205] "subtype6" "subtype5" "subtype1" "subtype5" "subtype6" "subtype6"
[211] "subtype2" "subtype6" "subtype5" "subtype6"
  [1] "subtype6" "subtype5" "subtype4" "subtype3" "subtype5" "subtype6"
  [7] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [13] "subtype6" "subtype5" "subtype6" "subtype3" "subtype2" "subtype2"
 [19] "subtype1" "subtype6" "subtype1" "subtype2" "subtype6" "subtype4"
 [25] "subtype5" "subtype5" "subtype3" "subtype6" "subtype6" "subtype5"
 [31] "subtype5" "subtype3" "subtype6" "subtype4" "subtype6" "subtype6"
 [37] "subtype6" "subtype5" "subtype5" "subtype6" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype6" "subtype5" "subtype3" "subtype3"
 [49] "subtype6" "subtype2" "subtype6" "subtype6" "subtype3" "subtype6"
 [55] "subtype4" "subtype5" "subtype3" "subtype1" "subtype6" "subtype3"
 [61] "subtype5" "subtype5" "subtype3" "subtype3" "subtype2" "subtype4"
 [67] "subtype6" "subtype4" "subtype6" "subtype6" "subtype6" "subtype5"
 [73] "subtype6" "subtype6" "subtype1" "subtype1" "subtype4" "subtype6"
 [79] "subtype1" "subtype1" "subtype3" "subtype6" "subtype5" "subtype5"
 [85] "subtype5" "subtype6" "subtype3" "subtype6" "subtype5" "subtype6"
 [91] "subtype1" "subtype3" "subtype4" "subtype5" "subtype6" "subtype1"
 [97] "subtype1" "subtype6" "subtype6" "subtype6" "subtype3" "subtype5"
[103] "subtype3" "subtype1" "subtype6" "subtype5" "subtype5" "subtype6"
[109] "subtype2" "subtype3" "subtype3" "subtype6" "subtype3" "subtype3"
[115] "subtype5" "subtype1" "subtype3" "subtype6" "subtype3" "subtype5"
[121] "subtype3" "subtype3" "subtype1" "subtype6" "subtype4" "subtype1"
[127] "subtype5" "subtype5" "subtype5" "subtype6" "subtype2" "subtype6"
[133] "subtype6" "subtype6" "subtype6" "subtype6" "subtype6" "subtype6"
[139] "subtype5" "subtype5" "subtype5" "subtype3" "subtype5" "subtype6"
[145] "subtype6" "subtype3" "subtype3" "subtype6" "subtype3" "subtype1"
[151] "subtype5" "subtype6" "subtype3" "subtype6" "subtype6" "subtype4"
[157] "subtype6" "subtype6" "subtype5" "subtype3" "subtype6" "subtype5"
[163] "subtype1" "subtype4" "subtype5" "subtype4" "subtype6" "subtype5"
[169] "subtype5" "subtype6" "subtype1" "subtype4" "subtype1" "subtype4"
[175] "subtype4" "subtype1" "subtype3" "subtype4" "subtype6" "subtype3"
[181] "subtype1" "subtype3" "subtype4" "subtype6" "subtype1" "subtype4"
[187] "subtype1" "subtype5" "subtype3" "subtype4" "subtype6" "subtype2"
[193] "subtype5" "subtype4" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype2" "subtype3" "subtype6" "subtype5" "subtype3" "subtype4"
[205] "subtype6" "subtype5" "subtype1" "subtype5" "subtype6" "subtype6"
[211] "subtype2" "subtype6" "subtype5" "subtype6"
  [1] "subtype6" "subtype5" "subtype4" "subtype3" "subtype5" "subtype6"
  [7] "subtype5" "subtype1" "subtype3" "subtype1" "subtype3" "subtype3"
 [13] "subtype6" "subtype5" "subtype6" "subtype3" "subtype2" "subtype2"
 [19] "subtype1" "subtype6" "subtype1" "subtype2" "subtype6" "subtype4"
 [25] "subtype5" "subtype5" "subtype3" "subtype6" "subtype6" "subtype5"
 [31] "subtype5" "subtype3" "subtype6" "subtype4" "subtype6" "subtype6"
 [37] "subtype6" "subtype5" "subtype5" "subtype6" "subtype5" "subtype5"
 [43] "subtype5" "subtype5" "subtype6" "subtype5" "subtype3" "subtype3"
 [49] "subtype6" "subtype2" "subtype6" "subtype6" "subtype3" "subtype6"
 [55] "subtype4" "subtype5" "subtype3" "subtype1" "subtype6" "subtype3"
 [61] "subtype5" "subtype5" "subtype3" "subtype3" "subtype2" "subtype4"
 [67] "subtype6" "subtype4" "subtype6" "subtype6" "subtype6" "subtype5"
 [73] "subtype6" "subtype6" "subtype1" "subtype1" "subtype4" "subtype6"
 [79] "subtype1" "subtype1" "subtype3" "subtype6" "subtype5" "subtype5"
 [85] "subtype5" "subtype6" "subtype3" "subtype6" "subtype5" "subtype6"
 [91] "subtype1" "subtype3" "subtype4" "subtype5" "subtype6" "subtype1"
 [97] "subtype1" "subtype6" "subtype6" "subtype6" "subtype3" "subtype5"
[103] "subtype3" "subtype1" "subtype6" "subtype5" "subtype5" "subtype6"
[109] "subtype2" "subtype3" "subtype3" "subtype6" "subtype3" "subtype3"
[115] "subtype5" "subtype1" "subtype3" "subtype6" "subtype3" "subtype5"
[121] "subtype3" "subtype3" "subtype1" "subtype6" "subtype4" "subtype1"
[127] "subtype5" "subtype5" "subtype5" "subtype6" "subtype2" "subtype6"
[133] "subtype6" "subtype6" "subtype6" "subtype6" "subtype6" "subtype6"
[139] "subtype5" "subtype5" "subtype5" "subtype3" "subtype5" "subtype6"
[145] "subtype6" "subtype3" "subtype3" "subtype6" "subtype3" "subtype1"
[151] "subtype5" "subtype6" "subtype3" "subtype6" "subtype6" "subtype4"
[157] "subtype6" "subtype6" "subtype5" "subtype3" "subtype6" "subtype5"
[163] "subtype1" "subtype4" "subtype5" "subtype4" "subtype6" "subtype5"
[169] "subtype5" "subtype6" "subtype1" "subtype4" "subtype1" "subtype4"
[175] "subtype4" "subtype1" "subtype3" "subtype4" "subtype6" "subtype3"
[181] "subtype1" "subtype3" "subtype4" "subtype6" "subtype1" "subtype4"
[187] "subtype1" "subtype5" "subtype3" "subtype4" "subtype6" "subtype2"
[193] "subtype5" "subtype4" "subtype3" "subtype3" "subtype3" "subtype3"
[199] "subtype2" "subtype3" "subtype6" "subtype5" "subtype3" "subtype4"
[205] "subtype6" "subtype5" "subtype1" "subtype5" "subtype6" "subtype6"
[211] "subtype2" "subtype6" "subtype5" "subtype6"
D5V2, continuous
D5V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   10
  subtype2    6    6
  subtype3   31   18
  subtype4   17    6
  subtype5   24   32
  subtype6   17   58
D5V4, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype3 subtype4 subtype5 subtype6 
       4        1        6        7 
 [1] "subtype5" "subtype5" "subtype3" "subtype6" "subtype6" "subtype5"
 [7] "subtype6" "subtype6" "subtype3" "subtype6" "subtype5" "subtype5"
[13] "subtype5" "subtype3" "subtype3" "subtype6" "subtype6"
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
D5V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    2
  subtype2   12    0
  subtype3   47    2
  subtype4   23    0
  subtype5   54    2
  subtype6   70    5
D5V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2    9    3
  subtype3   44    5
  subtype4   23    0
  subtype5   44   12
  subtype6   62   13

Clustering(6) Variable = MIRSEQ_CNMF
D6V1, survival
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[79] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[79] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype3"
[13] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype3" "subtype3"
[25] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[31] "subtype1" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype1"
[49] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[55] "subtype2" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[61] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype2"
[67] "subtype2" "subtype1" "subtype1" "subtype3" "subtype2" "subtype3"
[73] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[79] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[85] "subtype1"
D6V2, continuous
D6V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   23
  subtype2   18   11
  subtype3   11   21
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       11       21
  MALE         16       18       11
D6V4, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       1        2        3 
[1] "subtype3" "subtype3" "subtype3"
D6V5, multiclass
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass
D6V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37    2
  subtype2   29    0
  subtype3   30    2
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        2
  YES       37       29       30
D6V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    5
  subtype2   26    3
  subtype3   28    4
     clus
vv    subtype1 subtype2 subtype3
  NO         5        3        4
  YES       34       26       28

Clustering(7) Variable = MIRSEQ_CHIERARCHICAL
D7V1, survival
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[67] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[85] "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[67] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[85] "subtype1"
 [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[13] "subtype1" "subtype2" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
[31] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[37] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[43] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[49] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[55] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[61] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype3"
[67] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[73] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[79] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
[85] "subtype1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   20
  subtype2   11   20
  subtype3   14   15
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       20       15
  MALE         20       11       14
D7V4, continuous
D7V5, multiclass
D7V6, multiclass
D7V7, multiclass
D7V8, multiclass
D7V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39    1
  subtype2   29    2
  subtype3   28    1
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        1
  YES       39       29       28
D7V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    6
  subtype2   27    4
  subtype3   27    2
     clus
vv    subtype1 subtype2 subtype3
  NO         6        4        2
  YES       34       27       27
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
           "KARNOFSKY.PERFORMANCE.SCORE" 
                                      V5 
                     "HISTOLOGICAL.TYPE" 
                                      V6 
                           "PATHOLOGY.T" 
                                      V7 
                           "PATHOLOGY.N" 
                                      V8 
                   "PATHOLOGICSPREAD(M)" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V10 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
