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DOI-USGS / toxEval

The toxEval R-package includes a set of functions to analyze, visualize, and organize measured concentration data as it relates to chosen biological effects benchmarks. See https://doi-usgs.github.io/toxEval/ for more details
https://doi-usgs.github.io/toxEval/
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Gene information not included in toxcast 3.3 #388

Open lukeloken opened 4 years ago

lukeloken commented 4 years ago

https://github.com/USGS-R/toxEval/blob/6f3cf4feeec51b751582235c3c0943c148c7862e/R/toxEval.R#L124

Hey @ldecicco-USGS , I am looking at the end_point_info table associated with toxcast 3.3 I know you are working on updating this table and found a couple of issues with other columns. I noticed that this table does not have many gene's named or IDed. The table is also missing a few columns (e.g., intended_target_gene_symbol) that were in the version 3.2.

Anyway, I thought I would make a note here and let me know if I can help resolve the issue. The file referenced in this post looks to be on your machine rather than being in the package files.

ldecicco-USGS commented 4 years ago

Yeah, you'll have to download the summary files locally. The data is here: https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data Then you download and unzip the "ToxCast & Tox21 Summary Files for invitroDBv3.3"

Similarly, if you wanted to get the ACC stuff, you'd need to download and unzip the "ToxCast & Tox21 Data Spreadsheet for invitroDBv3.3".