Question: Error in TCGAquery of TCGAbiolinks Package
1
gravatar for Beginner
7 months ago by
Beginner50
Beginner50 wrote:

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 !!

 

 

ADD COMMENTlink modified 7 months ago by Benjamin Ostendorf70 • written 7 months ago by Beginner50
Answer: Error in TCGAquery of TCGAbiolinks Package
1
gravatar for Benjamin Ostendorf
7 months ago by
United States
Benjamin Ostendorf70 wrote:

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

ADD COMMENTlink written 7 months ago by Benjamin Ostendorf70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 318 users visited in the last hour