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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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Explanation of terms #23

Closed adomingues closed 4 years ago

adomingues commented 4 years ago

First of all thank you for developing this package. I am new to clinical analysis and this package and the vignettes / examples were a good start.

Regarding the survival analysis vignette, I have been trying to find a resource that explains / maps the variable names in the clinical data table and those used by the studies / Xena. For example the term OS.time doesn't show up in my searches of both the Xena portal or the Pan-Cancer Atlas. I am assuming time to remission, but it is just a guess. My question is there is a metadata table that explains what OS.time (and other terms) mean?

cheers, António

github-actions[bot] commented 4 years ago

Thanks for reporting, Shixiang will reply as soon as possible:)

ShixiangWang commented 4 years ago

@adomingues Sorry for the late reply. The vignette you read is out of date and I have updated it recently in my blog https://shixiangwang.github.io/home/en/post/ucscxenatools-201908/.

For the meaning of OS.time, you can read it in most of the datasets in UCSC Xena, such as LUAD

OS: overall survial PFI: progression-free interval DSS: disease-specific survival DFI: disease-free interval

OS data is the most important clinical data, OS.time indicates the time range from dignosis to patient's death.

adomingues commented 4 years ago

No worries @ShixiangWang. I am happy that now I am a bit more of an explanation about the terms. I read some papers and browsed the resource websites extensible but they have a lot of information.

Cheers.