在 R 中运行 GDC_prepare 时出现问题

Question

我正在尝试从 GDC 检索并准备一些数据，并且正在运行从该 YouTube 视频复制粘贴的以下代码：video。

以下是代码：

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)

运行最后一行代码后，我收到以下错误消息：

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) 

我不明白是什么导致了这个错误，因为我使用了与视频中相同的代码。

Answer 1

交叉发布并回答于https://support.bioconductor.org/p/9149780/

解决方案：更新软件包。

Answer 2

我可以知道您使用的是哪个 R 和 BiocManager 版本吗？我更新了还是有这个问题。