Error in TCGAquery of TCGAbiolinks Package
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Beginner ▴ 50
@beginner-15939
Last seen 11 months ago

Dear All,

I'm looking PAM50 molecular Subtypes of TCGA Breast RNA-Seq data. I'm using the following code. But I'm having an error with TCGAquery function. I have used similar code long back and it worked but now it is not working with TCGAquery function.

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

biocLite("TCGAbiolinks")
library(TCGAbiolinks)
cancer <- "BRCA"
PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
dataType <- "rsem.genes.results"
pathCancer <- "TCGAData/miRNA"

datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") 

Error in TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") : 
  could not find function "TCGAquery"

lsSample <- TCGAquery_samplesfilter(query = datQuery)

# get subtype information
dataSubt <- TCGAquery_subtype(tumor = cancer)
lumA <- dataSubt[which(dataSubt$PAM50.mRNA == "Luminal A"),1]
allSamples <- lsSample$IlluminaHiSeq_RNASeqV2 #1218 total samples

Any help please !!

 

 

software error bioconductor tcgabiolinks tcga r • 1.0k views
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@benjamin-ostendorf-15752
Last seen 20 days ago
United States

Hi Beginner,

after the transfer of the TCGA data to GDC the commands changed - try GDCquery instead of TCGAquery. Also make sure you have the latest version of TCGAbiolinks installed and take a look at the current vignette. 

Best,
Benjamin

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