[1] "started"
[1] "R version 2.15.3 (2013-03-01)"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/analysis.results.RData"
[1] "MUTSIG"
[1] "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
                                    V1.D 
                         "Time to Death" 
                                      V2 
                        "YEARS_TO_BIRTH" 
                                      V3 
                 "NEOPLASM_DISEASESTAGE" 
                                      V4 
                     "PATHOLOGY_T_STAGE" 
                                      V5 
                     "PATHOLOGY_N_STAGE" 
                                      V6 
                     "PATHOLOGY_M_STAGE" 
                                      V7 
                                "GENDER" 
                                      V8 
                     "HISTOLOGICAL_TYPE" 
                                      V9 
"RADIATIONS_RADIATION_REGIMENINDICATION" 
                                     V10 
                 "NUMBER_OF_LYMPH_NODES" 
                                     V11 
                                  "RACE" 
                                     V12 
                             "ETHNICITY" 
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[1] TRUE
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[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D2V6.png"
[1] FALSE
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[1] TRUE
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[1] TRUE
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[1] FALSE
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[1] TRUE
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[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V5.png"
[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V6.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V7.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V8.png"
[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V9.png"
[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V10.png"
[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V11.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D3V12.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D4V1.png"
[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D4V2.png"
[1] TRUE
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[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D4V4.png"
[1] TRUE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D4V5.png"
[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D4V6.png"
[1] TRUE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D5V5.png"
[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D122V5.png"
[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D122V6.png"
[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V1.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V2.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V3.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V4.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V5.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V6.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V7.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V8.png"
[1] TRUE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V9.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V10.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V11.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D149V12.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V1.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V2.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V3.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V4.png"
[1] TRUE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V5.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V6.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V7.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V8.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V9.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V11.png"
[1] TRUE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D150V12.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V1.png"
[1] TRUE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V2.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V3.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V4.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V6.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V7.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V8.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V9.png"
[1] FALSE
[1] "symlink"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events/BRCA-TP/15173309/D151V12.png"
[1] FALSE
