R语言下载完TCGA数据时，运行GDCprepare（）函数时，总是报C盘临时文件夹的一个错误

Question

 

 

代码如下：

library(pacman)
library(SummarizedExperiment)
library(TCGAbiolinks)
library(tidyverse)
library(magrittr)
library(data.table)
library(biomaRt)
 
 
 
projectPath = "D:/Project/sxkong_200415"  
dataPath = paste(projectPath, "Data", sep = "/")
if(!dir.exists(dataPath)) dir.create(dataPath)  
setwd(dataPath)
 
TCGAbiolinks:::getProjectSummary("TCGA-LIHC")
 
LIHC_query <- GDCquery(project = "TCGA-LIHC",
                       legacy = FALSE,
                       experimental.strategy = "RNA-Seq",
                       data.category = "Transcriptome Profiling",
                       data.type = "Gene Expression Quantification",
                       workflow.type = "HTSeq - FPKM-UQ")
 
GDCdownload(LIHC_query,files.per.chunk = 50)
 
dataAssy = GDCprepare(LIHC_query, summarizedExperiment = F)

R版本4.0.5  下载完数据运行 ： dataAssy = GDCprepare(LIHC_query, summarizedExperiment = F)时，

出现以下错误

 

> dataAssy = GDCprepare(LIHC_query, summarizedExperiment = F,directory = "GDCdata")
|                                                                                        |  0%                      错误: 'C:\Users\神的孩~1\AppData\Local\Temp\RtmpMl9OQE\file8a46f293134' does not exist.
Error in if (value == n) { : 参数长度为零
> dataAssy = GDCprepare(LIHC_query, summarizedExperiment = F,directory = "GDCdata")
|                                                                                        |  0%                      错误: 'C:\Users\神的孩~1\AppData\Local\Temp\RtmpMl9OQE\file8a45b9d58fd' does not exist.
Error in if (value == n) { : 参数长度为零
> dataAssy = GDCprepare(LIHC_query, summarizedExperiment = F)
|                                                                                        |  0%                      错误: 'C:\Users\神的孩~1\AppData\Local\Temp\RtmpMl9OQE\file8a4798e51d6' does not exist.
Error in if (value == n) { : 参数长度为零

求大神指点，小白一个，鼓捣两天了，实在是没辙了T T

Answer 1

可能是下载的数不完整，或者数据存放路径有问题。建议先将dataPath这个部分代码注释掉，这样来写：

BiocManager::install("TCGAbiolinks")
library(TCGAbiolinks)
?GDCquery
x<-getGDCprojects()$project_id

TCGAbiolinks:::getProjectSummary("TCGA-LIHC")
query<-GDCquery(project = "TCGA-LIHC",
                legacy=F,
                experimental.strategy ="RNA-Seq",
                data.category = "Transcriptome Profiling",
                data.type="Gene Expression Quantification",
                workflow.type="HTSeq - FPKM-UQ")

GDCdownload(query,files.per.chunk = 50)

dataAssy = GDCprepare(query, summarizedExperiment = F)

|=========================================================================|100%                      Completed after 47 s