Question: Asking about sample code in TCGAbiolinks
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gravatar for landscape95
2.5 years ago by
landscape95160
landscape95160 wrote:

I don't understand why there is no "Gene expression" in the data category on the web but the code still works. (add the library to it)

Code's Source: https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html

GDC project source: https://goo.gl/Q7GpT4

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)       
 # You can define a list of samples to query and download providing relative TCGA barcodes.
    listSamples <- c("TCGA-E9-A1NG-11A-52R-A14M-07","TCGA-BH-A1FC-11A-32R-A13Q-07",
                     "TCGA-A7-A13G-11A-51R-A13Q-07","TCGA-BH-A0DK-11A-13R-A089-07",
                     "TCGA-E9-A1RH-11A-34R-A169-07","TCGA-BH-A0AU-01A-11R-A12P-07",
                     "TCGA-C8-A1HJ-01A-11R-A13Q-07","TCGA-A7-A13D-01A-13R-A12P-07",
                     "TCGA-A2-A0CV-01A-31R-A115-07","TCGA-AQ-A0Y5-01A-11R-A14M-07")

    # Query platform Illumina HiSeq with a list of barcode 
    query <- GDCquery(project = "TCGA-BRCA", 
                      data.category = "Gene expression",
                      data.type = "Gene expression quantification",
                      experimental.strategy = "RNA-Seq",
                      platform = "Illumina HiSeq",
                      file.type = "results",
                      barcode = listSamples, 
                      legacy = TRUE)
tcgabiolinks • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by landscape95160
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