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shbrief / model_building

RAVmodel Building Workflows
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reference to non-existent build_gsea_DB.R script #2

Open lwaldron opened 2 years ago

lwaldron commented 2 years ago

I wanted to know how the GSEA is performed and saw it seems to be done with this line:

https://github.com/shbrief/model_building/blob/fbf985f436df9ee65f98abe9fc93f97b7411b9e2/07_Final_Model.R#L107

But the referenced file inst/scripts/build_gsea_DB.R in the GenomicSuperSignature package doesn't exist (looking here).

shbrief commented 2 years ago

Sorry, I've been moving around some accessory files/codes and haven't pushed them. Updated/correct file path is reflected in this commit: 1ab109315e3876acc8f31f247ab001bc78d9b802

shbrief commented 2 years ago

FYI, most of the scripts in this repository are more for in-house use, so some data files are not available. I've been working on making the whole RAVmodel building process a single workflow and plan to implement it in Nextflow (probably WDL as well). You can take a look at the current version here: 21ba4819be099e342a17d90be8691fac63581bea