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BioinformaticsFMRP / TCGAWorkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
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Got Error in getFirehoseData function #9

Open luoyuan1984 opened 5 years ago

luoyuan1984 commented 5 years ago

Hello, I am trying to run code below:

# Download GISTIC results
lastanalyzedate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",gistic2Date = lastanalyzedate)

# get GISTIC results
gistic.allbygene <- getData(gistic, type = "GISTIC", platform = "AllByGene")

I got an error like this: Error in getData(gistic, type = "GISTIC", platform = "AllByGene") : No data available for that type

I also tried to view gistic by view(gistic), but got another error: Error in if (more || nchar(output) > 80) { : missing value where TRUE/FALSE needed

I am using R:3.5.1 and RStudio:1.1.456 in Windows10 system.

Thank you.

tiagochst commented 4 years ago

It seems they updated the package. Thanks for pointing it out. The updated code is below.

library(RTCGAToolbox)
lastanalyzedate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",GISTIC = TRUE, gistic2Date = lastanalyzedate)

# get GISTIC results
gistic.allbygene <- getData(gistic, type = "GISTIC", platform = "AllByGene")
gistic.thresholedbygene <- getData(gistic, type = "GISTIC", platform = "ThresholdedByGene")

Sorry for the late reply. I did not get notified.