Entering edit mode
7.7 years ago
landscape95
▴
190
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)