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girke-lab / signatureSearch

R/Bioconductor package including the Gene Expression Signature Search (GESS), Function Enrichment Analysis (FEA) methods and supporting drug-target network construction for visualization
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BING genes #14

Closed macsennett closed 1 year ago

macsennett commented 1 year ago

When performing a query through the CLUE webapp, the up-regulated and down-regulated gene lists are filtered against a list of BING genes (Best INferred Gene space ). In your package, query genes are filtered against all reference database genes. I think a lot of people probably use your package with the CMap database, so I just wanted to point out this small difference in the query behavior. Would it be possible to implement a way to filter against the so-called BING genes in your package when using the CMap databases? Thanks for your work on this very useful package as well as the excellent vignettes.

brendangongol commented 1 year ago

Thank you for bringing this to my attention. I performed some updates to enable the specification of gene spaces when performing signatureSearching by passing the specified gene space onto the GeneType argument. These changes are reflected in the help file of the gess_lincs function and are currently staged in the girke-lab/signatureSearch github repository for installation. Please let me know if you encounter any errors or have additional feedback.