Comments (1)
ShixiangWang
commented on July 20, 2024
我重复不了该错误。
> downloadTCGA(project = "OV", data_type = "Phenotype", file_type = "Clinical Information", destdir = tempdir())
This will check url status, please be patient.
All downloaded files will under directory /var/folders/mx/rfkl27z90c96wbmn3_kjk8c80000gn/T//RtmpblndLG.
The 'trans_slash' option is FALSE, keep same directory structure as Xena.
Creating directories for datasets...
Downloading TCGA.OV.sampleMap/OV_clinicalMatrix.gz
试开URL’https://tcga.xenahubs.net/download/TCGA.OV.sampleMap/OV_clinicalMatrix.gz'
Content type 'application/gzip' length 113764 bytes (111 KB)
==================================================
downloaded 111 KB
能否使用以下命令安装最新版本的UCSCXenaTools然后再尝试下？
remotes::install_github("ShixiangWang/UCSCXenaTools")
看你的报错显示是使用了libcurl导致的报错，你可以使用method参数指定下载的方法：
downloadTCGA(project = "OV", data_type = "Phenotype", file_type = "Clinical Information", destdir = tempdir(), method = "curl")
具体可以运行?download.file()查看method一栏的说明，有多种下载方法可以指定。
第二个问题：GDC是美国为了整合癌症数据资源弄得一个数据端口，它不仅仅只包含TCGA。GDC TCGA使用的是hg38版本的参考基因组，而TCGA是hg19版本的基因组，所以它们的差别是参考基因组以及数据版本的不同，根据自己的需要选择使用。你现在使用的是https://shixiangwang.github.io/UCSCXenaTools/articles/USCSXenaTools.html#download-tcga-data-with-readable-options部分提供的函数，只支持hg19版本的数据下载。
另外推荐你使用标准的下载流程下载数据
即
XeneGenerate()
XenaQuery()
XenaDownload()
等函数。
from ucscxenatools.
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