Genome_Wide_SNP_6 - question support bioconductor

Genome_Wide_SNP_6.R

# install last version
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

query <- TCGAquery(tumor = "GBM",platform = "Genome_Wide_SNP_6", level = 3 )

samples <- TCGAquery_samplesfilter(query = query)

# Which samples are Primary Solid Tumor
dataSmTP <- TCGAquery_SampleTypes(barcode = samples$Genome_Wide_SNP_6,
                                  typesample = "TP")
# Which samples are Solid Tissue Normal
dataSmNT <- TCGAquery_SampleTypes(barcode = samples$Genome_Wide_SNP_6,
                                  typesample ="NT")
# get clinical data

TCGAdownload(data = query,
             path = "gwsnp", type="hg19.seg",
             samples =c(dataSmTP,dataSmNT))

dataAssyCNV <- TCGAprepare(query = query,
                           dir = "gwsnp",
                           save = TRUE,
                           type="cnv_hg19",
                           summarizedExperiment = TRUE,
                           samples = c(dataSmTP,dataSmNT),
                           filename = paste0("Genome_Wide_SNP_6.rda"))