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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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missing "OS", "OS.time", "OS.unit", "RFS", "RFS.time", "RFS.unit" columns in the downloaded clinical infomration file from TCGA #22

Closed danshu closed 4 years ago

danshu commented 4 years ago

Hello,

I'm following this tutorial "TCGA Pan-cancer data download" (https://xsliulab.github.io/tumor-immunogenicity-score/#data-download-and-preprocessing) to download and clean TCGA clinical data. However, columns like "OS", "OS.time", "OS.unit", "RFS", "RFS.time", "RFS.unit" are expected to be but absent in the clinical information files. Is this due to updates of the "UCSCXenaTools" package?

Best, Danshu

github-actions[bot] commented 4 years ago

Free to ask any questions or suggestions :)

ShixiangWang commented 4 years ago

@danshu Thanks for reporting. I checked and found this is due to the updates of UCSC Xena for Clinical data. The recent version is 2019-12-06, you can view this LUAD cohort. I did not find any version control, so we can't download older version data now. You have to do some dirty clean data for yourself, or you can use the tidy data from https://github.com/XSLiuLab/tumor-immunogenicity-score/blob/master/report/results/TCGA_tidy_Clinical.RData.

Hope it help.

Best, Shixiang

danshu commented 4 years ago

@ShixiangWang Thanks!