Filter TCGAbiolinks by Gene in Query
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jam526 • 0
@jam526-22332
Last seen 14 months ago

Here is the basic example for downloading rna-seq data for gbm from TCGA using TCGABiolinks.

  # mRNA pipeline: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/
query.exp.hg38 <- GDCquery(project = "TCGA-GBM", 
                  data.category = "Transcriptome Profiling", 
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - FPKM-UQ",
                  barcode =  c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"))
GDCdownload(query.exp.hg38)
expdat <- GDCprepare(query = query.exp.hg38,
                     save = TRUE, 
                     save.filename = "exp.rda")

My question is: is there a way to filter for what genes we want to include in the downloaded summarized experiment object? What if I just want to look at, for example, expression of ribosomal proteins and don't want to download the thousands of other genes? Am thinking of using TCGABiolinks in a shiny app where the user can select the genes they want, so not downloading everything will be a lot faster.

If this is not possible with TCGAbiolinks is there another package that has the functionality I'm looking for?

tcgabiolinks filtering gdc TCGABiolinks rnaseq • 123 views
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