Download of full ACC and BRCA datasets, GBM IMPACT341

cBioPortal tests

# to run this using Docker from the command line on the stock Bioconductor image:
# docker run -it bioconductor/bioconductor_docker:latest R

BiocManager::install("cBioPortalData")
library(cBioPortalData)

#acc_tcga full data pack
system.time(accpack <- cBioDataPack("acc_tcga")) #~10 seconds
accpack

#brca_tcga full data pack
system.time(brcapack <- cBioDataPack("brca_tcga")) #~109 seconds
brcapack

# acc_tcga IMPACT341 Reverse Phase Protein Array (RPPA) and Copy Number Alterations (CNA)
# takes ~1 minute
cBio <- cBioPortal()
system.time(acc341 <- cBioPortalData(api = cBio, by = "hugoGeneSymbol", studyId = "acc_tcga",
    genePanelId = "IMPACT341",
    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
))
acc341

# second time is much faster due to local caching (~1 second)
system.time(acc341 <- cBioPortalData(cBio, studyId = "acc_tcga", 
    genePanelId = "IMPACT341",
    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA")
)) 
acc341