
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.81.4078/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.81.4078/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/347506/BLCA-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BLCA-TP/2585709/1.GDAC_clinicalDataPicker.Finished/BLCA-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-nV=Nozzle.R1", "-OP=MUTSIG", "-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=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=128, in cluster file=28, common to both=28
[1]  3 28
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5              23 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5              23 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               24 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               24 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONTHERAPY"                      
[11] "KARNOFSKYPERFORMANCESCORE"             
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "NUMBERPACKYEARSSMOKED"                 
[14] "STOPPEDSMOKINGYEAR"                    
[15] "TOBACCOSMOKINGHISTORYINDICATOR"        
[16] "DISTANT.METASTASIS"                    
[17] "LYMPH.NODE.METASTASIS"                 
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "TUMOR.STAGECODE"                       
[20] "NEOPLASM.DISEASESTAGE"                 
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 28 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
         389           NA           NA           NA          363           NA 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20V TCGA-BT-A20W TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
          NA           NA           NA           59           88           61 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
          NA           14           13           NA           NA          219 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
          77           NA          273          271 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'NUMBERPACKYEARSSMOKED':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'STOPPEDSMOKINGYEAR':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR.STAGECODE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                            "GENDER"                        
 [3] "NUMBERPACKYEARSSMOKED"          "STOPPEDSMOKINGYEAR"            
 [5] "TOBACCOSMOKINGHISTORYINDICATOR" "DISTANT.METASTASIS"            
 [7] "LYMPH.NODE.METASTASIS"          "NUMBER.OF.LYMPH.NODES"         
 [9] "TUMOR.STAGECODE"                "NEOPLASM.DISEASESTAGE"         
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1  T2 T2B  T3 T3A T3B  T4 T4A T4B 
  1   1   4   5   7   5   1   3   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 28 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=11, binary=FALSE, numeric=TRUE
STOPPEDSMOKINGYEAR, nv=6, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=3, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2            0 1
  TP53 MUTATED   3 8
  TP53 WILD-TYPE 8 9
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
             8              9 
$`TP53 MUTATED`
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20U TCGA-C4-A0EZ 
        2.66        19.00        26.10        12.16         8.61         8.98 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AB 
        2.04         0.43         2.53         2.14         8.91 

$`TP53 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q 
       12.79         7.33         6.58        11.93        17.85        19.46 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
       14.89         5.06         8.35         1.94         2.89         2.01 
TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A7 
        0.46        12.92         4.90         7.20         8.98 

  TP53 MUTATED TP53 WILD-TYPE 
          0.43           0.46 
  TP53 MUTATED TP53 WILD-TYPE 
         26.10          19.46 
  TP53 MUTATED TP53 WILD-TYPE 
          8.61           7.33 
[1] "0.4 - 26.1 (8.6)" "0.5 - 19.5 (7.3)"
    TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BT-A0S7 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A20O 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-BT-A20P     TCGA-BT-A20Q     TCGA-BT-A20T     TCGA-BT-A20U 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-BT-A20V     TCGA-BT-A20W     TCGA-C4-A0EZ     TCGA-C4-A0F0 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-C4-A0F1     TCGA-C4-A0F6     TCGA-C4-A0F7     TCGA-CF-A1HR 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-CF-A1HS     TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A7     TCGA-DK-A1AB 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BT-A0S7 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A20O 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-BT-A20P     TCGA-BT-A20Q     TCGA-BT-A20T     TCGA-BT-A20U 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-BT-A20V     TCGA-BT-A20W     TCGA-C4-A0EZ     TCGA-C4-A0F0 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-C4-A0F1     TCGA-C4-A0F6     TCGA-C4-A0F7     TCGA-CF-A1HR 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-CF-A1HS     TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A7     TCGA-DK-A1AB 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BT-A0S7 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-BT-A0YX     TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A20O 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-BT-A20P     TCGA-BT-A20Q     TCGA-BT-A20T     TCGA-BT-A20U 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-BT-A20V     TCGA-BT-A20W     TCGA-C4-A0EZ     TCGA-C4-A0F0 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-C4-A0F1     TCGA-C4-A0F6     TCGA-C4-A0F7     TCGA-CF-A1HR 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-CF-A1HS     TCGA-CU-A0YN     TCGA-CU-A0YO     TCGA-CU-A0YR 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DK-A1A3     TCGA-DK-A1A5     TCGA-DK-A1A7     TCGA-DK-A1AB 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  TP53 MUTATED    4  7
  TP53 WILD-TYPE  6 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4    7
  TP53 WILD-TYPE    6   11
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            4              6
  MALE              7             11
D1V4, continuous
D1V5, continuous
D1V6, continuous
                vv
clus             M0 M1 MX
  TP53 MUTATED    7  1  3
  TP53 WILD-TYPE 15  0  2
D1V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0            7             15
  M1            1              0
  MX            3              2
                vv
clus             N0 N1 N2 NX
  TP53 MUTATED    6  1  3  0
  TP53 WILD-TYPE 10  1  5  1
D1V8, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0            6             10
  N1            1              1
  N2            3              5
  NX            0              1
D1V9, continuous
D1V10, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         0        2         3        5
  TP53 WILD-TYPE       1        2         7        6
D1V11, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              0              1
  STAGE II             2              2
  STAGE III            3              7
  STAGE IV             5              6

Clustering(2) Variable = FBXW7 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    3  2
  FBXW7 WILD-TYPE  8 15
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5              23 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2              15 
$`FBXW7 MUTATED`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-C4-A0F0 TCGA-C4-A0F1 
        7.33        11.93        12.16         1.94         2.89 

$`FBXW7 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       12.79         2.66         6.58        19.00        26.10        17.85 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-C4-A0EZ 
       19.46        14.89         8.61         5.06         8.35         8.98 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO 
        2.01         2.04         0.46         0.43        12.92         4.90 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
        7.20         2.53         2.14         8.98         8.91 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.94            0.43 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          12.16           26.10 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
           7.33            8.35 
[1] "1.9 - 12.2 (7.3)" "0.4 - 26.1 (8.3)"
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BT-A0S7 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A0YX      TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A20O 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-BT-A20P      TCGA-BT-A20Q      TCGA-BT-A20T      TCGA-BT-A20U 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-BT-A20V      TCGA-BT-A20W      TCGA-C4-A0EZ      TCGA-C4-A0F0 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-C4-A0F7      TCGA-CF-A1HR 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-CF-A1HS      TCGA-CU-A0YN      TCGA-CU-A0YO      TCGA-CU-A0YR 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-DK-A1A3      TCGA-DK-A1A5      TCGA-DK-A1A7      TCGA-DK-A1AB 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  FBXW7 MUTATED    2  3
  FBXW7 WILD-TYPE  8 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      2    3
  FBXW7 WILD-TYPE    8   15
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             2               8
  MALE               3              15
D2V4, continuous
D2V5, continuous
D2V6, continuous
                 vv
clus              M0 M1 MX
  FBXW7 MUTATED    4  0  1
  FBXW7 WILD-TYPE 18  1  4
D2V7, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  M0             4              18
  M1             0               1
  MX             1               4
                 vv
clus              N0 N1 N2 NX
  FBXW7 MUTATED    5  0  0  0
  FBXW7 WILD-TYPE 11  2  8  1
D2V8, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             5              11
  N1             0               2
  N2             0               8
  NX             0               1
D2V9, continuous
D2V10, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FBXW7 MUTATED         0        1         4        0
  FBXW7 WILD-TYPE       1        3         6       11
D2V11, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0               1
  STAGE II              1               3
  STAGE III             4               6
  STAGE IV              0              11

Clustering(3) Variable = NFE2L2 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED    2  2
  NFE2L2 WILD-TYPE  9 15
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               24 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2               15 
$`NFE2L2 MUTATED`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20U TCGA-C4-A0F6 
        7.33        11.93         8.61         2.01 

$`NFE2L2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.79         2.66         6.58        19.00        26.10        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-C4-A0EZ 
       17.85        19.46        14.89         5.06         8.35         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN 
        1.94         2.89         2.04         0.46         0.43        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB 
        4.90         7.20         2.53         2.14         8.98         8.91 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            2.01             0.43 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           11.93            26.10 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           7.970            7.775 
[1] "2.0 - 11.9 (8.0)" "0.4 - 26.1 (7.8)"
      TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BT-A0S7 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N       TCGA-BT-A20O 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T       TCGA-BT-A20U 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-BT-A20V       TCGA-BT-A20W       TCGA-C4-A0EZ       TCGA-C4-A0F0 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C4-A0F1       TCGA-C4-A0F6       TCGA-C4-A0F7       TCGA-CF-A1HR 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CF-A1HS       TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A7       TCGA-DK-A1AB 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BT-A0S7 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N       TCGA-BT-A20O 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T       TCGA-BT-A20U 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-BT-A20V       TCGA-BT-A20W       TCGA-C4-A0EZ       TCGA-C4-A0F0 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C4-A0F1       TCGA-C4-A0F6       TCGA-C4-A0F7       TCGA-CF-A1HR 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CF-A1HS       TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A7       TCGA-DK-A1AB 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BT-A0S7 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N       TCGA-BT-A20O 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T       TCGA-BT-A20U 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" 
      TCGA-BT-A20V       TCGA-BT-A20W       TCGA-C4-A0EZ       TCGA-C4-A0F0 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C4-A0F1       TCGA-C4-A0F6       TCGA-C4-A0F7       TCGA-CF-A1HR 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CF-A1HS       TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DK-A1A3       TCGA-DK-A1A5       TCGA-DK-A1A7       TCGA-DK-A1AB 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
[1] "hr=" "1.4"
D3V2, continuous
D3V3, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    4  0
  NFE2L2 WILD-TYPE  6 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    0
  NFE2L2 WILD-TYPE    6   18
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              4                6
  MALE                0               18
D3V4, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2               11 
      TCGA-BL-A0C8       TCGA-BL-A13J       TCGA-BT-A20J       TCGA-BT-A20N 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C4-A0EZ       TCGA-C4-A0F0       TCGA-C4-A0F1       TCGA-CU-A0YN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CU-A0YR       TCGA-DK-A1A3       TCGA-DK-A1A5 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
D3V5, continuous
D3V6, continuous
                  vv
clus               M0 M1 MX
  NFE2L2 MUTATED    4  0  0
  NFE2L2 WILD-TYPE 18  1  5
D3V7, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  M0              4               18
  M1              0                1
  MX              0                5
                  vv
clus               N0 N1 N2 NX
  NFE2L2 MUTATED    4  0  0  0
  NFE2L2 WILD-TYPE 12  2  8  1
D3V8, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              4               12
  N1              0                2
  N2              0                8
  NX              0                1
D3V9, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2               18 
      TCGA-BL-A0C8       TCGA-BL-A13J       TCGA-BT-A0S7       TCGA-BT-A20J 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A20N       TCGA-BT-A20O       TCGA-BT-A20P       TCGA-BT-A20Q 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-BT-A20T       TCGA-BT-A20V       TCGA-BT-A20W       TCGA-CU-A0YN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CU-A0YO       TCGA-CU-A0YR       TCGA-DK-A1A3       TCGA-DK-A1A5 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DK-A1A7       TCGA-DK-A1AB 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
D3V10, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         0        0         4        0
  NFE2L2 WILD-TYPE       1        4         6       11
D3V11, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                0                1
  STAGE II               0                4
  STAGE III              4                6
  STAGE IV               0               11
                            V1.D                               V2 
                 "Time to Death"                            "AGE" 
                              V3                               V4 
                        "GENDER"          "NUMBERPACKYEARSSMOKED" 
                              V5                               V6 
            "STOPPEDSMOKINGYEAR" "TOBACCOSMOKINGHISTORYINDICATOR" 
                              V7                               V8 
            "DISTANT.METASTASIS"          "LYMPH.NODE.METASTASIS" 
                              V9                              V10 
         "NUMBER.OF.LYMPH.NODES"                "TUMOR.STAGECODE" 
                             V11 
         "NEOPLASM.DISEASESTAGE" 
> q(save="no")
