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:video.
Below is the code:
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 after running the last line of code 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)
I do not understand what is causing this error since I'm using the same code as in the video.
Cross-posted and answered at https://support.bioconductor.org/p/9149780/
Solution: Update packages.