Filter TCGAbiolinks by Gene in Query
0
0
Entering edit mode
jam526 • 0
@jam526-22332
Last seen 3.9 years 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 • 955 views
ADD COMMENT

Login before adding your answer.

Traffic: 833 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6