TCGA data 다운로드 관련

https://www.biostars.org/p/96209/

https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#tcgaanalyze_preprocessing-preprocessing-of-gene-expression-data-illuminahiseq_rnaseqv2

source("https://bioconductor.org/biocLite.R")

biocLite("TCGAbiolinks")

library(TCGAbiolinks)

# Gene expression download

luadexp <- GDCquery(project = "TCGA-LUAD",

                    data.category = "Transcriptome Profiling" ,

                    data.type = "Gene Expression Quantification",

                    workflow.type  = "HTSeq - FPKM-UQ",

                    experimental.strategy = "RNA-Seq",legacy = F)

GDCdownload(luadexp);luadexp2=GDCprepare(luadexp)

library(SummarizedExperiment)

luadmat=assay(luadexp2)

cluad=GDCquery_clinic('TCGA-LUAD') # clinical information을 다운받을 수 있음.

GBM데이터 받기용

# download gene expression data
query.exp.hg19 <- GDCquery(project = "TCGA-GBM",
                           data.category = "Transcriptome Profiling",
                           data.type = "Gene Expression Quantification",
                           experimental.strategy='RNA-seq',
                           workflow.type  = "HTSeq - FPKM",
                           legacy = F)

RPPA data download하는 법
tmp=GDCquery(project ="TCGA-LGG" ,platform = 'MDA_RPPA_Core',legacy = T,
             data.category = 'Protein expression')
GDCdownload(tmp)
lgg_rppa=GDCprepare(tmp)