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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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Filter pathways by gene symbol #80

Closed gabrielodom closed 5 years ago

gabrielodom commented 5 years ago

Per the website discussion for http://bio-bigdata.hrbmu.edu.cn/PathACT/ with Steven, Lily (@lxw391), and Yunpeng, we need to add a function that queries a trimmed pathway collection by a gene symbol.

My idea is that we could add a "symbol" argument to getPathwayCollection() and getTrimPathwayCollection(). This argument would default to NULL. If a character string is supplied, we would query each pathway in the collection for the pathways that contain that symbol, then return only those pathways. Also, we could make it more general and query the pathways for more than one symbol at once (but it would be an AND condition rather than an OR). In theory, this should also work for regions (when we apply this to CoMethDMR).

gabrielodom commented 5 years ago

We added the function WhichPathways() and its helper function Contains() to the package. We can search for pathways that single symbols, multiple symbols with AND joining, multiple symbols with OR, joining, and partial lead-matching for single symbols (to find pathways that contain any gene from a gene family or any CpG site in a 100 or 1000-width block).

gabrielodom commented 5 years ago

@lxw391, please check out the new functionality. It might be helpful for CoMethDMR and rnaEditr as well.