在R中运行GDC_prepare时出现的问题

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英文:

Problems when running GDC_prepare in R

问题

我尝试从GDC检索和准备一些数据,我正在运行以下代码,我是从这个YouTube视频中复制粘贴的:video

以下是代码:

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

# 获取项目列表
gdcprojects <- getGDCprojects()

# 构建查询
query_TCGA <- GDCquery(project = 'TCGA-BRCA',
                       data.category = 'Transcriptome Profiling')
output_query_TCGA <- getResults(query_TCGA)

# 构建查询以检索基因表达数据
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)

# 下载数据 - GDCdownload
GDCdownload(query_TCGA)

# 准备数据
tcga_brca_data <- GDCprepare(query_TCGA)

在运行代码的最后一行之后,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) 

我不理解这个错误是什么原因,因为我正在使用与视频中相同的代码。

英文:

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 &lt;- getGDCprojects()


# building a query
query_TCGA &lt;- GDCquery(project = &#39;TCGA-BRCA&#39;,
                       data.category = &#39;Transcriptome Profiling&#39;)
output_query_TCGA &lt;- getResults(query_TCGA)


# build a query to retrieve gene expression data ------------
query_TCGA &lt;- GDCquery(project = &#39;TCGA-BRCA&#39;,
                       data.category = &#39;Transcriptome Profiling&#39;,
                       experimental.strategy = &#39;RNA-Seq&#39;,
                       workflow.type = &#39;STAR - Counts&#39;,
                       access = &#39;open&#39;,
                       barcode = c(&#39;TCGA-LL-A73Y-01A-11R-A33J-07&#39;, &#39;TCGA-E2-A1IU-01A-11R-A14D-07&#39;,&#39;TCGA-AO-A03U-01B-21R-A10J-07&#39;))

getResults(query_TCGA)

# download data - GDCdownload
GDCdownload(query_TCGA)


# prepare data
tcga_brca_data &lt;- 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&#39;t subset columns past the end.
i Locations 2, 3, and 4 don&#39;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 &lt;- vroom(...)
  problems(dat) 
2: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat &lt;- vroom(...)
  problems(dat) 
3: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat &lt;- vroom(...)
  problems(dat) 

I do not understand what is causing this error since I'm using the same code as in the video.

答案1

得分: 0

跨贴并在https://support.bioconductor.org/p/9149780/上回答。

解决方案:更新软件包。

英文:

Cross-posted and answered at https://support.bioconductor.org/p/9149780/

Solution: Update packages.

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  • 本文由 发表于 2023年2月27日 04:38:26
  • 转载请务必保留本文链接:https://go.coder-hub.com/75574873.html
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