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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/6068629/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/6154386/BLCA-TP.merged_data.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=BLCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=BLCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/6154386/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/6068629/transformed.cor.cli.txt"

nPatients in clinical file=186, in cluster file=28, common to both=28
[1]  1 28
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "GLEASON_SCORE"                         
[21] "PSA_VALUE"                             
[22] "DAYS_TO_PSA"                           
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 28 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        1219           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          700 
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          560          271 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'PSA_VALUE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'DAYS_TO_PSA':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[7] "NUMBERPACKYEARSSMOKED" "NUMBER.OF.LYMPH.NODES" "GLEASON_SCORE"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 28 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 1  5 17  5 
[1] "table(vv)"
vv
T1+T2    T3    T4 
    6    17     5 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 1  5 17  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1+T2    T3    T4 
    6    17     5 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
16  2  8 
[1] "table(vv)"
vv
   N0 N1+N2 
   16    10 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
16  2  8 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 16

$Class1_nSamples
[1] 10

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   16    10 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=11, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=3, binary=FALSE, numeric=TRUE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    3  8
  TP53 WILD-TYPE  7 10
  TP53 MUTATED TP53 WILD-TYPE 
            11             17 
  TP53 MUTATED TP53 WILD-TYPE 
             8             10 
$`TP53 MUTATED`
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20U TCGA-C4-A0EZ 
        2.66        19.00        32.84        12.16        14.93         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 
       40.08         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        23.01 
TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A7 
        0.46        12.92         4.90         7.20        18.41 

  TP53 MUTATED TP53 WILD-TYPE 
          0.43           0.46 
  TP53 MUTATED TP53 WILD-TYPE 
         32.84          40.08 
  TP53 MUTATED TP53 WILD-TYPE 
          8.91           8.35 
[1] "0.4 - 32.8 (8.9)" "0.5 - 40.1 (8.3)"
    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=" "1.5"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         0        2         3        5
  TP53 WILD-TYPE       1        2         7        6
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              0              1
  STAGE II             2              2
  STAGE III            3              7
  STAGE IV             5              6
                vv
clus             T1+T2 T3 T4
  TP53 MUTATED       2  6  3
  TP53 WILD-TYPE     4 11  2
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1+T2            2              4
  T3               6             11
  T4               3              2
                vv
clus             N0 N1+N2
  TP53 MUTATED    6     4
  TP53 WILD-TYPE 10     6
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0               6             10
  N1+N2            4              6
                vv
clus             M0 M1 MX
  TP53 MUTATED    7  1  3
  TP53 WILD-TYPE 15  0  2
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0            7             15
  M1            1              0
  MX            3              2
D1V7, 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
D1V8, continuous
D1V9, continuous
D1V10, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1              5 
    TCGA-BT-A20T     TCGA-BT-A20W     TCGA-CU-A0YN     TCGA-CU-A0YO 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CU-A0YR 
"TP53 WILD-TYPE" 
> q(save="no")
