Error when running GDC_prepare
0
0
Entering edit mode
@4bb5d1af
Last seen 6 months ago
Sweden

I'm trying to retrieve and prepare some data from GDC and I'm running the following code which I copy-pasted from this YouTube video: https://www.youtube.com/watch?v=UWXv9dUpxNE


library(TCGAbiolinks)
library(tidyverse)
library(maftools)
library(pheatmap)
library(SummarizedExperiment)


# get a list of projects
gdcprojects <- getGDCprojects()


# building a query
query_TCGA <- GDCquery(project = 'TCGA-BRCA',
                       data.category = 'Transcriptome Profiling')
output_query_TCGA <- getResults(query_TCGA)


# build a query to retrieve gene expression data ------------
query_TCGA <- GDCquery(project = 'TCGA-BRCA',
                       data.category = 'Transcriptome Profiling',
                       experimental.strategy = 'RNA-Seq',
                       workflow.type = 'STAR - Counts',
                       access = 'open',
                       barcode = c('TCGA-LL-A73Y-01A-11R-A33J-07', 'TCGA-E2-A1IU-01A-11R-A14D-07','TCGA-AO-A03U-01B-21R-A10J-07'))

getResults(query_TCGA)

# download data - GDCdownload
GDCdownload(query_TCGA)


# prepare data
tcga_brca_data <- GDCprepare(query_TCGA)

#And i get the following error message

leted after 0 s 
Error in `map()`:
i In index: 1.
i With name: 1.
Caused by error in `y[, 2:4]`:
! Can't subset columns past the end.
i Locations 2, 3, and 4 don't exist.
i There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
Warning messages:
1: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat) 
2: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat) 
3: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)
TCGAbiolinks • 2.0k views
ADD COMMENT
1
Entering edit mode

Hi, your code is working on my side. Please, what TCGAbiolinks version you have installed ?

enter image description here

ADD REPLY
0
Entering edit mode

Oh, okay thank you so much. I checked and updated my version of R and BiocManager and now the code is working, what a rookie misstake. Thank you so much for the response.

ADD REPLY

Login before adding your answer.

Traffic: 965 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