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BioinformaticsFMRP / TCGAWorkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
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Example data for TCGA Workflow: #10

Closed Dokmen closed 5 years ago

Dokmen commented 5 years ago

Hi, I checked your page https://bioconductor.org/packages/release/data/experiment/vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html

I wrote issue for RTCGAworkflow but they wanted to write you. in your page, there are codes for gistic file. 

`library(RTCGAToolbox)
# Download GISTIC results
lastAnalyseDate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",gistic2_Date = lastAnalyseDate)

# get GISTIC results
gistic.allbygene <- getData(gistic,type = "GISTIC", CN = "All")`

gistic.allbygene <- getData(gistic,type = "GISTIC", CN = "All")
Error in getData(gistic, type = "GISTIC", CN = "All") : 
  unused argument (CN = "All")
tiagochst commented 5 years ago

It seems the RTCGAToolbox package had some changes. Thew new code is below:

library(RTCGAToolbox)
lastAnalyseDate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",gistic2_Date = lastAnalyseDate, GISTIC = TRUE)
gistic.allbygene <- getData(gistic,type = "GISTIC", platform = "AllByGene")
gistic.thresholedbygene <- getData(gistic,type = "GISTIC", platform = "ThresholdedByGene")