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update RTCGAToolbox code #2

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update RTCGAToolbox code #2

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6 changes: 3 additions & 3 deletions vignettes/TCGAWorkflowData.Rmd
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Expand Up @@ -68,12 +68,12 @@ Download and save a subset of GBM GISTIC results from GDAC firehose.
library(RTCGAToolbox)
# Download GISTIC results
lastAnalyseDate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",gistic2_Date = lastAnalyseDate)
gistic <- getFirehoseData("GBM", gistic2Date = lastAnalyseDate, GISTIC = TRUE)

# get GISTIC results
gistic.allbygene <- getData(gistic,type = "GISTIC", CN = "All")
gistic.allbygene <- getData(gistic,type = "GISTIC", platform = "AllByGene")
gistic.allbygene <- gistic.allbygene[1:10,]
gistic.thresholedbygene <- getData(gistic,type = "GISTIC", CN = "Thresholed")
gistic.thresholedbygene <- getData(gistic,type = "GISTIC", platform = "ThresholdedByGene")
gistic.thresholedbygene <- gistic.thresholedbygene[1:10,]
save(gistic.allbygene,gistic.thresholedbygene,file = "GBMGistic.rda", compress = "xz")
```
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