
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/1552855/1.GDAC_mergedClustering.Finished/LUAD.mergedcluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD/1445470/1.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=286, common to both=282
[1]   7 282
[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  4  5 
37 41 62 29 41 
 1  2  3  4  5 
37 41 62 29 41 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2 
100 110 
  1   2 
100 110 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
37 29 29 
 1  2  3 
37 29 29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
28 28 39 
 1  2  3 
28 28 39 
[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 282 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-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         181          264         2595         1147         1491          863 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
        1073          354         1357          158           NA          574 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
         581          400          529          103          480          400 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246          311          253          196          189 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         140          106          498          208            9          102 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          236           95          165           82         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
          NA         1110           NA          298          162          153 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
          50          557           NA          531          535          418 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896           NA         1314 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         457          369          395          150            1           NA 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
          NA         2174         1485          455          785          297 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          245          282          267         1091         2369 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         653          257          460          285          135          373 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
         349           NA           NA           NA           NA           NA 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
          NA         1015           NA          255         1068          970 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1374           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
         992           24           NA         1238           NA           28 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        1475           NA           NA           NA           67           NA 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          NA         1826           NA         1233         2161         1170 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          61           18           34           NA            4           95 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
          40           39           31           31           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
         197           21            3         1728          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1685         1126           NA         2550            3          926 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         507         1145          223           30           60           18 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          62           18           NA           27           21          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-71-6725 
         154          186          690          414          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        1599          711          911          467           14           40 
TCGA-73-4676 TCGA-73-4677 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 
         122           38           NA           NA           NA           NA 
TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
          NA           NA           NA           NA           NA         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
          NA         1201          760           NA           NA           NA 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
          NA         1220          678          214           NA         6812 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 
         327          881           NA          994           NA           NA 
TCGA-80-5611 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
          NA           NA           NA           11           27            7 
TCGA-86-7714 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          NA           37           NA            1           39           35 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          11           NA          819          127           28           31 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-97-7546 TCGA-97-7547 
         127           34            2          163          963         1435 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-99-7458 
        1476         1331          263          181           NA          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=172,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	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=69,	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 282 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 
 76 166  23  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 76 166  23  15 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
 T1  T2  T3  T4 
 76 166  23  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 76 166  23  15 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
164  59  51   1 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  164    59    52 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
 N0  N1  N2  N3 
164  59  51   1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  164    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" "subtype4" "subtype3" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype5"
 [19] "subtype1" "subtype1" "subtype5" "subtype5" "subtype2" "subtype5"
 [25] "subtype4" "subtype3" "subtype3" "subtype2" "subtype5" "subtype5"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [37] "subtype3" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype2" "subtype3" "subtype5" "subtype3" "subtype2"
 [49] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
 [67] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype5"
 [73] "subtype5" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [79] "subtype2" "subtype3" "subtype2" "subtype1" "subtype4" "subtype3"
 [85] "subtype3" "subtype5" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype5" "subtype5" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[109] "subtype5" "subtype3" "subtype3" "subtype5" "subtype4" "subtype5"
[115] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype1" "subtype3" "subtype5" "subtype2"
[127] "subtype4" "subtype5" "subtype5" "subtype3" "subtype5" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype4" "subtype3" "subtype5"
[139] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[145] "subtype1" "subtype5" "subtype5" "subtype1" "subtype2" "subtype5"
[151] "subtype5" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[157] "subtype5" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
[163] "subtype1" "subtype3" "subtype5" "subtype3" "subtype2" "subtype5"
[169] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[175] "subtype5" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[181] "subtype5" "subtype4" "subtype4" "subtype3" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype5"
 [19] "subtype1" "subtype1" "subtype5" "subtype5" "subtype2" "subtype5"
 [25] "subtype4" "subtype3" "subtype3" "subtype2" "subtype5" "subtype5"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [37] "subtype3" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype2" "subtype3" "subtype5" "subtype3" "subtype2"
 [49] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
 [67] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype5"
 [73] "subtype5" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [79] "subtype2" "subtype3" "subtype2" "subtype1" "subtype4" "subtype3"
 [85] "subtype3" "subtype5" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype5" "subtype5" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[109] "subtype5" "subtype3" "subtype3" "subtype5" "subtype4" "subtype5"
[115] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype1" "subtype3" "subtype5" "subtype2"
[127] "subtype4" "subtype5" "subtype5" "subtype3" "subtype5" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype4" "subtype3" "subtype5"
[139] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[145] "subtype1" "subtype5" "subtype5" "subtype1" "subtype2" "subtype5"
[151] "subtype5" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[157] "subtype5" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
[163] "subtype1" "subtype3" "subtype5" "subtype3" "subtype2" "subtype5"
[169] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[175] "subtype5" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[181] "subtype5" "subtype4" "subtype4" "subtype3" "subtype3"
  [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
  [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype4" "subtype2" "subtype1" "subtype4" "subtype1" "subtype5"
 [19] "subtype1" "subtype1" "subtype5" "subtype5" "subtype2" "subtype5"
 [25] "subtype4" "subtype3" "subtype3" "subtype2" "subtype5" "subtype5"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [37] "subtype3" "subtype1" "subtype2" "subtype4" "subtype1" "subtype4"
 [43] "subtype4" "subtype2" "subtype3" "subtype5" "subtype3" "subtype2"
 [49] "subtype5" "subtype3" "subtype3" "subtype3" "subtype5" "subtype3"
 [55] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
 [61] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
 [67] "subtype4" "subtype3" "subtype4" "subtype1" "subtype2" "subtype5"
 [73] "subtype5" "subtype1" "subtype1" "subtype3" "subtype4" "subtype5"
 [79] "subtype2" "subtype3" "subtype2" "subtype1" "subtype4" "subtype3"
 [85] "subtype3" "subtype5" "subtype1" "subtype2" "subtype2" "subtype2"
 [91] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
 [97] "subtype2" "subtype2" "subtype1" "subtype5" "subtype5" "subtype1"
[103] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype4"
[109] "subtype5" "subtype3" "subtype3" "subtype5" "subtype4" "subtype5"
[115] "subtype3" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
[121] "subtype3" "subtype2" "subtype1" "subtype3" "subtype5" "subtype2"
[127] "subtype4" "subtype5" "subtype5" "subtype3" "subtype5" "subtype3"
[133] "subtype3" "subtype3" "subtype1" "subtype4" "subtype3" "subtype5"
[139] "subtype4" "subtype3" "subtype3" "subtype4" "subtype1" "subtype1"
[145] "subtype1" "subtype5" "subtype5" "subtype1" "subtype2" "subtype5"
[151] "subtype5" "subtype2" "subtype1" "subtype2" "subtype4" "subtype1"
[157] "subtype5" "subtype1" "subtype3" "subtype2" "subtype5" "subtype5"
[163] "subtype1" "subtype3" "subtype5" "subtype3" "subtype2" "subtype5"
[169] "subtype2" "subtype1" "subtype2" "subtype4" "subtype3" "subtype2"
[175] "subtype5" "subtype4" "subtype3" "subtype2" "subtype3" "subtype5"
[181] "subtype5" "subtype4" "subtype4" "subtype3" "subtype3"
D4V2, continuous
D4V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   15
  subtype2   25   16
  subtype3   25   37
  subtype4    9   20
  subtype5   16   25
D4V4, continuous
[1] "Remove cluster labels:" "subtype4"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       3        7        2        2 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype3" "subtype3" "subtype2" "subtype3"
D4V5, multiclass
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
D4V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    3
  subtype2   40    1
  subtype3   58    4
  subtype4   27    2
  subtype5   40    1
D4V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30    7
  subtype2   38    3
  subtype3   46   16
  subtype4   27    2
  subtype5   35    6

Clustering(5) Variable = MRNASEQ_CHIERARCHICAL
D5V1, survival
  [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[121] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[145] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[163] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
  [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[121] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[145] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[163] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
  [1] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
  [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [13] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [19] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [31] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
 [37] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
 [49] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
 [55] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
 [61] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [67] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [73] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
 [79] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
 [85] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
 [91] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
 [97] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[103] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[109] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[115] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[121] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[127] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[133] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1" "subtype2"
[139] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype2"
[145] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[151] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[157] "subtype2" "subtype1" "subtype1" "subtype1" "subtype2" "subtype2"
[163] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[169] "subtype1" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1"
[175] "subtype2" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
[181] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[1] "hr=" "2"  
D5V2, continuous
D5V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58   42
  subtype2   39   71
        clus
vv       subtype1 subtype2
  FEMALE       42       71
  MALE         58       39
D5V4, continuous
D5V5, multiclass
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
D5V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    5
  subtype2  104    6
     clus
vv    subtype1 subtype2
  NO         5        6
  YES       95      104
D5V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   85   15
  subtype2   91   19
     clus
vv    subtype1 subtype2
  NO        15       19
  YES       85       91

Clustering(6) Variable = MIRSEQ_CNMF
D6V1, survival
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[79] "subtype2" "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[79] "subtype2" "subtype1"
 [1] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[13] "subtype3" "subtype2" "subtype2" "subtype1" "subtype2" "subtype1"
[19] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[25] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[31] "subtype3" "subtype3" "subtype1" "subtype3" "subtype3" "subtype1"
[37] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[43] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[49] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[55] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[61] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
[67] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype2"
[73] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype3"
[79] "subtype2" "subtype1"
D6V2, continuous
D6V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   23
  subtype2   18   11
  subtype3   11   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       11       18
  MALE         14       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   35    2
  subtype2   29    0
  subtype3   27    2
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        2
  YES       35       29       27
D6V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31    6
  subtype2   26    3
  subtype3   26    3
     clus
vv    subtype1 subtype2 subtype3
  NO         6        3        3
  YES       31       26       26

Clustering(7) Variable = MIRSEQ_CHIERARCHICAL
D7V1, survival
 [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype1" "subtype1"
 [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype1" "subtype1"
 [1] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[13] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[19] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[25] "subtype1" "subtype3" "subtype1" "subtype2" "subtype3" "subtype3"
[31] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype2"
[37] "subtype2" "subtype3" "subtype1" "subtype1" "subtype2" "subtype2"
[43] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[49] "subtype3" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[61] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[67] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype1"
[73] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype3"
[79] "subtype1" "subtype1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   13
  subtype2   14   14
  subtype3   14   25
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13       14       25
  MALE         15       14       14
D7V4, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype3 
       2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
D7V5, multiclass
D7V6, multiclass
D7V7, multiclass
D7V8, multiclass
D7V9, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   26    2
  subtype3   37    2
     clus
vv    subtype1 subtype2 subtype3
  NO         0        2        2
  YES       28       26       37
D7V10, binary
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25    3
  subtype2   25    3
  subtype3   33    6
     clus
vv    subtype1 subtype2 subtype3
  NO         3        3        6
  YES       25       25       33
                                    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")
